The central dogma of biology holds that genetic information normally flows from DNA to RNA to protein. As a consequence it has been generally assumed that genes generally code for proteins, and that proteins fulfil not only most structural and catalytic but also most regulatory functions, in all cells, from microbes to mammals. However, the latter may not be the case in complex organisms. A number of startling observations about the extent of non-protein-coding RNA (ncRNA) transcription in the higher (...) eukaryotes and the range of genetic and epigenetic phenomena that are RNA-directed suggests that the traditional view of the structure of genetic regulatory systems in animals and plants may be incorrect. ncRNA dominates the genomic output of the higher organisms and has been shown to control chromosome architecture, mRNA turnover and the developmental timing of protein expression, and may also regulate transcription and alternative splicing. This paper re-examines the available evidence and suggests a new framework for considering and understanding the genomic programming of biological complexity, autopoletic development and phenotypic variation. BioEssays 25:930-939,2003. (C) 2003 Wiley Periodicals, Inc. (shrink)

Insulators play a central role in subdividing the chromosome into a series of discrete topologically independent domains and in ensuring that enhancers and silencers contact their appropriate target genes. In this review we first discuss the general characteristics of insulator elements and their associated protein factors. A growing collection of insulator proteins have been identified including a family of proteins whose expression is developmentally regulated. We next consider several unexpected discoveries that require us to completely rethink how insulators function (and (...) how they can best be assayed). These discoveries also require a reevaluation of how insulators might restrict or orchestrate (by preventing or promoting) interactions between regulatory elements and their target genes. We conclude by connecting these new insights into the mechanisms of insulator action to dynamic changes in the three‐dimensional topology of the chromatin fiber and the generation of specific patterns of gene activity during development and differentiation. (shrink)

Spatially and temporally restricted expression of Hox genes requires multiple mechanisms at both the transcriptional and the post-transcriptional levels. New insight into this precise expression mechanism comes from recent findings of a novel sense–antisense miRNA combination from the bithorax complex of Drosophila melanogaster.1-4 These two miRNAs encoded from the same locus target 3′ untranslated regions of anterior hox genes, Antp, Ubx and abd-A to establish the dominance of posterior hox gene Abd-B in its expression domain. Such double-edge tools, (...) sense–antisense miRNA combinations, also operate at multiple loci in the genome implicating their wider impact on the post-transcriptional gene regulation in eukaryotes. BioEssays 30:1058–1061, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

Each of the homeotic genes of the bithorax complex of Drosophila defines the identities of more than one body segment. The mechanisms by which this occurs have been elusive. In a recent report, Castelli‐Gair and Akam(1) analyze in detail the control of parasegment 5 and parasegment 6 identities by the bithorax complex gene Ubx. Their results indicate that differences in the spatial and temporal expression patterns of Ubx are critical in determining differences between these parasegments. However, (...) dose effects observed by others indicate that parasegment‐specific differences in the level of Ubx expression are also important. For the other BX‐C genes, parasegment‐specific expression of protein isoforms, or combinatorial control dependent on the expression patterns of other spatially restricted regulators, may also play a role. (shrink)

Micro RNAs (miRNAs) have been shown to control many cellular processes including developmental timing in different organisms. The prediction that miRNAs are involved in regulating hox genes of flies and mouse is quite a recent idea and is supported by the finding that mir‐196 represses Hoxb8 gene expression. The non‐coding regions that encode these miRNAs are also conserved across species in the same way as other mechanisms that regulate expression of hox genes. On the contrary, until now no homeotic phenotype, (...) a hallmark of any hox gene mutation, had been associated with any hox miRNA. Recent work on bithorax complex miRNA (miR–iab‐4–5p) shows, for the first time, that miRNAs can lead to homeotic transformation. This miRNA regulates Ultrabithorax (Ubx) and results in the transformation of haltere to wing.1 This study unveils a new complexity and finesse to the regulation of hox gene expression pattern that is needed for determining the anteroposterior body axis in all bilaterians. BioEssays 28: 445–448, 2006. © 2006 Wiley Periodicals, Inc. (shrink)

In recent years, the method of the complex network has been applied to various fields. Dynamics research in complex networks is also an important branch. There are many types of research into dynamic complex network, but few scholars use bibliometrics to study it. Therefore, this paper adopts the method of bibliometrics to analyze the development history and status quo of dynamic complex network, providing a summary description of this research field. We used CiteSpace and Pajek to (...) analyze 2936 relevant papers on the website of Web of Science and further interpreted and summarized the analysis results. To fully show the bibliometric results, we further derive the productive countries, institutions, sources, and authors and some main research directions in the dynamic complex network research. The research results show that the dynamic complex network research method was applied to various fields after the dynamic research method had been integrated into the complex network. According to the subject analysis of the cited papers, we find that the dynamic complex network method has been widely used in various subjects. Through emergent analysis, we found that the latest hot research trends are the study of infectious diseases and applications in neural networks. At the same time, through the main path analysis, we find the essential literature to elaborate on the development context of a dynamic complex network at different time points. This paper gives a comprehensive analysis of dynamic complex network research and provides some enlightenment for the future research direction. (shrink)

This paper investigates the effects of (surface) DP-internal quantifying expressions on semantic interpretation. In particular, I investigate two syntactic constructions in which an adjective takes scope out of its embedding DP, thus raising an interesting question for strict compositionality. Regarding the first construction, I follow Larson (1999) and assume that the adjective incorporates into the determiner of its DP, forming a complex quantifier [D+A]. I present new evidence in favor of this analysis. Since Larson's semantic analysis of complex (...) quantifiers [D+A] makes a wrong prediction, I propose an alternative, empirically more adequate analysis that treats D+A compounds as pluractional quantifiers in the sense of Lasersohn (1995). Finally, I turn to the second construction, arguing that – despite superficial similarities to the first construction - it should not be analyzed in terms of complex quantifier formation, but in terms of LF-movement of the adjective to Spec,DP. The discussion suggests that there is more than one way for DP-internal modifiers to take DP-external scope in natural language. (shrink)

How can our societies be stabilized in a crisis? Why do we enjoy and understand Shakespeare? Why are fruitflies uniform? How do omnivorous eating habits aid our survival? What makes the Mona Lisa's smile beautiful? How do women keep their social structures intact? -- Could there possibly be a single answer to all these questions? This book shows that the statement 'weak links stabilize complex systems' provides the key to understanding each of these intriguing puzzles, and many others too. (...) The author...uses weak (low affinity, low probability) interactions as a thread to introduce a vast variety of networks from proteins to economics and ecosystems. --From publisher description. (shrink)

This theoretical expose explores the complex notion of argumentative style, which has so far been largely neglected in argumentation theory. After an introduction of the problems involved, the theoretical tools for identifying the properties of the discourse in which an argumentative style manifests itself are explained from a pragma-dialectical perspective and a theoretical definition of argumentative style is provided that does full justice to its role in argumentative discourse. The article concludes with a short reflection upon the next steps (...) that need to be taken in argumentation theory in further substantiating the notion of argumentative style. (shrink)

This book employs contemporary philosophy, scientific research, and clinical reports to argue that pain, though real, is not an appropriate object of scientific generalisations or an appropriate target for medical intervention. Each pain experience is instead complex and idiosyncratic in a way which undermines scientific utility. In addition to contributing novel arguments and developing a novel position on the nature of pain, the book provides an interdisciplinary overview of dominant models of pain. The author lays the needed groundwork for (...) improved models and targeted treatments at a time when pain science, pain medicine, and philosophy are explicitly searching for both and failing to find them. The Complex Reality of Pain will be of interest to a broad range of researchers and students, including those working in philosophy of mind, philosophy of science, cognitive science, neuroscience, medicine, health, cognitive and behavioural psychology, and pain science. (shrink)

This theoretical expose explores the complex notion of argumentative style, which has so far been largely neglected in argumentation theory. After an introduction of the problems involved, the theoretical tools for identifying the properties of the discourse in which an argumentative style manifests itself are explained from a pragma-dialectical perspective and a theoretical definition of argumentative style is provided that does full justice to its role in argumentative discourse. The article concludes with a short reflection upon the next steps (...) that need to be taken in argumentation theory in further substantiating the notion of argumentative style. (shrink)

In terms of Groenendijk and Stokhof’s (1984) formalization of exhaustive interpretation, many conversational implicatures can be accounted for. In this paper we justify and generalize this approach. Our justification proceeds by relating their account via Halpern and Moses’ (1984) non-monotonic theory of ‘only knowing’ to the Gricean maxims of Quality and the first sub-maxim of Quantity. The approach of Groenendijk and Stokhof (1984) is generalized such that it can also account for implicatures that are triggered in subclauses not entailed by (...) the whole complex sentence. (shrink)

The aim of the presented article is to provide an in-depth analysis of the adequacy of designating Penrose as a complex Pythagorean in view of his much more common designation as a Platonist. Firstly, the original doctrine of the Pythagoreans will be briefly surveyed with the special emphasis on the relation between the doctrine of this school and the teachings of the late Platonic School as well as its further modifications. These modifications serve as the prototype of the contemporary (...) claims of the mathematicity of the Universe. Secondly, two lines of Penrose’s arguments in support of his unique position on the ontology of the mathematical structures will be presented: their existence independent of the physical world in the atemporal Platonic realm of pure mathematics and the mathematical structures as the patterns governing the workings of the physical Universe. In the third step, a separate line of arguments will be surveyed that Penrose advances in support of the thesis that the complex numbers seem to suit these patterns with exceptional adequacy. Finally, the appropriateness of designation Penrose as a complex Pythagorean will be assessed with the special emphasis on the suddle threshold between his unique position and that of the adherents of the mathematicity of the Universe. (shrink)

The logic of genetic discovery has changed little over time, but the focus of biology is shifting from simple genotype–phenotype relationships to complex metabolic, physiological, developmental, and behavioral traits. In light of this, the traditional reductionist view of individual genes as privileged difference‐making causes of phenotypes is re‐examined. The scope and nature of genetic effects in complex regulatory systems, in which dynamics are driven by regulatory feedback and hierarchical interactions across levels of organization are considered. This review argues (...) that it is appropriate to treat genes as specific actual difference‐makers for the molecular regulation of gene expression. However, they are often neither stable, proportional, nor specific as causes of the overall dynamic behavior of regulatory networks. Dynamical models, properly formulated and validated, provide the tools to probe cause‐and‐effect relationships in complex biological systems, allowing to go beyond the limitations of genetic reductionism to gain an integrative understanding of the causal processes underlying complex phenotypes. (shrink)

I relate plural quantification, and predicate logic where predicates do not need a fixed number of argument places, to the part-whole relation. For more on these themes see later work by Boolos, Lewis, and Oliver & Smiley.

Research on future-oriented mental time travel (FMTT) is highly active yet somewhat unruly. I believe this is due, in large part, to the complexity of both the tasks used to test FMTT and the concepts involved. Extraordinary care is a necessity when grappling with such complex and perplexing metaphysical constructs as self and time and their co-instantiation in memory. In this review, I first discuss the relation between future mental time travel and types of memory (episodic and semantic). I (...) then examine the nature of both the types of self-knowledge assumed to be projected into the future and the types of temporalities that constitute projective temporal experience. Finally, I argue that a person lacking episodic memory should nonetheless be able to imagine a personal future by virtue of (a) the fact that semantic, as well as episodic, memory can be self-referential, (b) autonoetic awareness is not a prerequisite for FMTT, and (c) semantic memory does, in fact, enable certain forms of personally-oriented FMTT. (shrink)

The complex systems approach (CSA) to characterizing cognitive function is purported to underlie a conceptual and methodological revolution by its proponents. I examine one central claim from each of the contributed papers and argue that the provided examples do not justify calls for radical change in how we do cognitive science. Instead, I note how currently available approaches in ‘‘standard’’ cognitive science are adequate (or even more appropriate) for understanding the CSA provided examples.

I am going to describe a variant formulation of classical extensional first-order logic and contrast it with the standard formulation. The formulation I will give is in one clear sense equivalent to the standard one, and it is a routine task to show that it is equivalent to it in this sense. So one might regard my formulation as a mere notational variation. But there are also ways in which the two formulations I will contrast are not equivalent, and I (...) will argue that these ways reflect an important conceptual difference between them. The differences become more important as one generalizes or extends classical logic in various ways, but they are there even in the classical systems. (shrink)

In our 2004, we introduced two games in the spirit of the St Petersburg game, the Pasadena and Altadena games. As these latter games lack an expectation, we argued that they pose a paradox for decision theory. Terrence Fine has shown that any finite valuations for the Pasadena, Altadena, and St Petersburg games are consistent with the standard decision-theoretic axioms. In particular, one can value the Pasadena game above the other two, a result that conflicts with both our intuitions and (...) dominance reasoning. We argue that this result, far from resolving the Pasadena paradox, should serve as a reductio of the standard theory, and we consequently make a plea for new axioms for a revised theory. We also discuss a proposal by Kenny Easwaran that a gamble should be valued according to its 'weak expectation', a generalization of the usual notion of expectation. (shrink)

Cumulative cultural evolution is often claimed to be distinctive of human culture. Such claims are typically supported with examples of complex and historically late-appearing technologies. Yet by taking these as paradigm cases, researchers unhelpfully lump together different ways that culture accumulates. This article has two aims: (a) to distinguish four types of cultural accumulation: adaptiveness, complexity, efficiency, and disparity and (b) to highlight the epistemic implications of taking complex hominin technologies as paradigmatic instances of cumulative culture. Addressing these (...) issues both clarifies the cumulative culture concept and demonstrates the importance of further cumulative culture research into non-human animals and ancestral hominins. (shrink)

The aim of this paper is to respond to recent discussion of, and objections to, the libertarian view of free will I have developed in many works over the past four decades. The issues discussed all have a bearing on the central question of how one might make sense of a traditional free will requiring indeterminism in the light of modern science. This task involves, among other things, avoiding all traditional libertarian appeals to unusual forms of agency or causation that (...) cannot be accounted for by ordinary modes of explanation familiar to the natural and human sciences. Doing this, I argue, requires piecing together a “complex tapestry” of ideas and arguments that involve rethinking many traditional assumptions about free will. The paper also argues that one cannot get to the heart of historical debates about free will without distinguishing different kinds of freedom, different senses of will, and different notions of control, among other distinctions. I especially focus here on different notions of freedom and control that are necessary to make sense of free will. (shrink)

In my short commentary, I dwell on the distinction between basic and complex empathy, and suggest that a basic perception-based form of empathy might point to the existence of a type of social understanding that is more direct and more fundamental than the types of social cognition normally addressed by simulation theory and theory theory.

Ecologist Richard Levins argues population biologists must trade‐off the generality, realism, and precision of their models since biological systems are complex and our limitations are severe. Steven Orzack and Elliott Sober argue that there are cases where these model properties cannot be varied independently of one another. If this is correct, then Levins's thesis that there is a necessary trade‐off between generality, precision, and realism in mathematical models in biology is false. I argue that Orzack and Sober's arguments fail (...) since Levins's thesis concerns the pragmatic features of model building not just the formal properties of models. (shrink)

This essay examines liminality as space of which dominant groups largely are ignorant. The limen is at the edge of hardened structures, a place where transgression of the reigning order is possible. As such, it both offers communicative openings and presents communicative impasses to liminal beings. For the limen to be a coalitional space, complex communication is required. This requires praxical awareness of one's own multiplicity and a recognition of the other's opacity that does not attempt to assimilate it (...) into one's own familiar meanings. Refusing the assumption of transparency and operating with relational identities, the complex communication that occurs in the limen—often invisible to dominant groups—can enable genuine coalition and effective resistance to domination. (shrink)

Ellie Anderson had always known that she wanted to have children. Her mother, Louise, was aware of this wish. Ellie was designated male at birth, but according to news sources, identified as a girl from the age of three. She was hoping to undergo gender reassignment surgery at 18, but died unexpectedly at only 16, leaving Louise grappling not only with the grief of losing her daughter, but with a complex legal problem. Ellie had had her sperm frozen before (...) starting hormone treatment, specifically so that she would retain the chance of becoming a parent after her gender reassignment. Ellie had considered what might happen to the sperm if she died and was adamant that her children should be brought into the world. She made her mother promise to ensure that this would happen. But according to UK law, Ellie’s mother has no legal right to retain her sperm, or to use it to fulfil Ellie’s wishes. In this paper, we raise several key ethical questions on this case, namely: does a refusal to bring Ellie’s children into the world wrong her posthumously? Is Ellie’s mother morally entitled to use her daughter’s sperm as Ellie wished? Should the fact that Ellie was a minor at the time of her death or the fact that she was transgendered undermine her wish to have children? Can Ellie become a parent posthumously? We consider how these complex ethical questions could be approached. (shrink)

The study of complex systems, although an interdisciplinary endeavor, is considered as an integrating part of physical sciences. Contrary to the historical fact that the field is already mature, it still lacks a clear and unambiguous definition of its main object of study. Here, I propose a definition of complex systems based on the conceptual clarifications made by Edgar Morin about the bidirectional non-separability of parts and whole produced by the nature of interactions. Then, a complex system (...) is defined as the system where there is a bidirectional non-separability between the identities of the parts and the identity of the whole. Thus, not only the identity of the whole is determined by the constituent parts, but also the identity of the parts are determined by the whole due to the nature of their interactions. This concept allows, as shown in the paper, to derive some of the main properties that such systems must have as well as to propose its mathematical formalization. (shrink)

Some demonstrative expressions, those we might term ‘bare demonstratives’, appear without any appended descriptive content (e.g. occurrences of ‘this’ or ‘that’ simpliciter). However, it seems that the majority of demonstrative occurrences do not follow this model. ‘Complex demonstratives’ is the collective term I shall use for phrases formed by adjoining one or more common nouns to a demonstrative expression (e.g. ‘that cat’, ‘this happy man’) and I will call the combination of predicates immediately concatenated with the demonstrative in such (...) phrases the ‘matrix’ of the expression. The question, then, is how we should construe the logical form of such expressions within a semantic theory for our language; and I wish to suggest that some recent answers to this question are, in fact, mistaken. The structure of the paper is as follows: first, I wish to highlight two (often underlying) assumptions about the nature of noun phrases in general, and suggest that, if they are both adopted, they apparently constrain the possible accounts of the logical form of complex demonstratives to just three options. The second and third parts of the paper will be concerned with expanding these options and arguing that none of them are adequate; thus the major part of the paper is concerned with the negative claim that the most obvious moves to make in this area must actually fail on closer inspection. The fourth and final section will then (very briefly) sketch the positive thesis of the paper: that we can deliver a clear and cohesive account of complex demonstratives, armed simply with elements which we will draw from David Kaplan’s theory of demonstratives, but only at the cost of rejecting (or at least refining) one assumption we recognised initially. (shrink)

Standard semantic theories predict that non-deictic readings for complex demonstratives should be much more widely available than they in fact are. If such readings are the result of a lexical ambiguity, as Kaplan (in: Almog, Perry, Wettstein (eds) Themes from Kaplan, Oxford University Press, Oxford, 1977) and others suggest, we should expect them to be available wherever a definite description can be used. The same prediction follows from ‘hidden argument’ theories like the ones described by King (Complex Demonstratives: (...) a Quantificational Account, MIT Press, Cambridge, 2001) and Elbourne (Situations and Individuals, MIT Press, Cambridge, 2005). Wolter (That’s That; the Semantics and Pragmatics of Demonstrative Noun Phrases. Ph.D. thesis, University of California at Santa Cruz, 2006), however, has shown that complex demonstratives admit non-deictic interpretations only when a precise set of structural constrains are met. In this paper, I argue that Wolter’s results, properly understood, upend the philosophical status quo. They fatally undermine the ambiguity theory and demand a fundamental rethinking of the hidden argument approach. (shrink)

This paper proposes a Cournot game organized by three competing firms adopting bounded rationality. According to the marginal profit in the past time step, each firm tries to update its production using local knowledge. In this game, a firm’s preference is represented by a utility function that is derived from a constant elasticity of substitution production function. The game is modeled by a 3-dimensional discrete dynamical system. The equilibria of the system are numerically studied to detect their complex characteristics (...) due to difficulty to get an explicit form for those equilibria. For the proposed utility function, some cases with different value parameters are considered. Numerical simulations are used to provide an experimental evidence for the complex behavior of the evolution of the system. The obtained results show that the system loses its stability due to different types of bifurcations. (shrink)

Complex vocal learning, the capacity to imitate new sounds, underpins the evolution of animal vocal cultures and song dialects and is a key prerequisite for human speech and song. Due to its relevance for the understanding of cultural evolution and the biology and evolution of language and music, the trait has gained much scholarly attention. However, while we have seen tremendous progress with respect to our understanding of its morphological, neurological and genetic aspects, its peculiar phylogenetic distribution has remained (...) elusive. Intriguingly, animals as distinct as hummingbirds and humpback whales share well-developed vocal learning capacity in common with humans, while this ability is quite limited in nonhuman primates. Yet, solving this ‘vocal learning conundrum’ may shed light on the constraints ancestral humans overcame to unleash their vocal capacities. To this end I consider major constraints and functions that have been proposed. I highlight an especially promising ecological constraint, namely the spatial dimensionality of the environment. Based on an informal comparative review, I suggest that complex vocal learning is associated with three-dimensional habitats such as air and water. I argue that this is consistent with recent theoretical advances—i.e., the coercion-avoidance and dimensionality hypotheses—and with the long-standing hypothesis that mate choice is a major driver of the evolution and origin of complex vocal learning. However, I stress that multiple functions may apply and that quantitative phylogenetic comparative methods should be employed to finally resolve the issue. (shrink)

Biological reproduction is a material process of intertwined, recursive propagule generation and development, assuming that development produces simple life cycles. Most organisms, however, have more or less complex life cycles. Here, I attempt to reconcile recent articulations of a reproducer account with traditional approaches to complex life cycles by generalizing genetic demarcation criteria for life cycle generations in terms of the “scaffolded” development of hybrid reproducers. I argue that scaffolding provides a general method for identifying developmental bottlenecks and (...) suggests in turn a new way of understanding developmental reaction norms. (shrink)

This paper makes and defends four interrelated claims. First: most conscious experiences are complex in the sense that they have discernible constituent structure with discernible parts that can feature as parts of other experiences, and might occur as standalone experiences. Second: complex experiences have simple constituents that have no further discernible parts. Third: the phenomenal quality of having a complex experience is jointly determined by the phenomenal quality of its simple constituents plus the phenomenal structure simple constituents (...) are organised into. And fourth: physical descriptions can convey all the relevant information about the discernible phenomenal structure of conscious experiences. The combination of these four claims tells us that there is no further explanatory gap related to the phenomenal quality of complex experiences given that one is familiar with the phenomenal qualities of the simple parts constituting the complex experience in question, and that it is possible to acquire knowledge about the phenomenal quality of yet unexperienced complex experiences on the basis of previous acquaintances with constituent parts plus structural information. That is, the paper argues for a ‘summation’ model of phenomenal qualities. (shrink)

In the last 20 years, a stream of research emerged under the label of „complex problem solving“ (CPS). This research was intended to describe the way people deal with complex, dynamic, and intransparent situations. Complex computer-simulated scenarios were as stimulus material in psychological experiments. This line of research lead to subtle insights into the way how people deal with complexity and uncertainty. Besides these knowledge-rich, realistic, intransparent, complex, dynamic scenarios with many variables, a second line of (...) research used more simple, knowledge-lean scenarios with a low number of variables („minimal complex systems“, MCS) that have been proposed recently in problem-solving research for the purpose of educational assessment. In both cases, the idea behind the use of microworlds is to increase validity of problem solving tasks by presenting interactive environments that can be explored and controlled by participants while pursuing certain action goals. The main argument presented here is: both types of systems - CPS and MCS – can only be dealt with successfully if causal dependencies between input and output variables are identified and used for system control. System knowledge is necessary for control and intervention. But CPS and MCS differ in their way of how causal dependencies are identified and how the mental model is constructed; therefore, they cannot be compared directly to each other with respect to the cognitive processes that are necessary for solving the tasks. Knowledge-poor MCS tasks address only a small fraction of the cognitive processes and structures needed for knowledge-rich CPS situations. (shrink)