The evolution of functionally referential meaning in a structured world

Animal communication systems serve to transfer both motivational information--about the intentions or emotional state of the signaler--and referential information--about external objects. Although most animal calls seem to deal primarily with motivational information, those with a substantial referential component are particularly interesting because they invite comparison with words in human language. We present a game-theoretic model of the evolution of communication in a "structured world", where some situations may be more similar to one another than others, and therefore require similar responses. We find that breaking the symmetry in this way creates the possibility for a diverse array of evolutionarily stable communication systems. When the number of signals is limited, as in alarm calling, the system tends to evolve to group together situations which require similar responses. We use this observation to make some predictions about the situations in which primarily motivational or referential communication systems will evolve.     

The amazing world of bacterial structured RNAs

The discovery of several new structured non-coding RNAs in bacterial and archaeal genomes and metagenomes raises burning questions about their biological and biochemical functions.     

Sexual reproduction prevails in a world of structured resources in short supply

We present a model for the maintenance of sexual reproduction based on the availability of resources, which is the strongest factor determining the growth of populations. The model compares completely asexual species to species that switch between asexual and sexual reproduction (sexual species). Key features of the model are that sexual reproduction sets in when resources become scarce, and that at a given place only a few genotypes can be present at the same time. We show that under a wide range of conditions the sexual species outcompete the asexual ones. The asexual species win only when survival conditions are harsh and death rates are high, or when resources are so little structured or consumer genotypes are so manifold that all resources are exploited to the same extent. These conditions largely represent the conditions in which sexuals predominate over asexuals in the field.     

Intersectionality and mediated cultural production in a globalized post-colonial world

Abstract

This paper aims to demonstrate how intersectionality provides an important conceptual tool to analyse practices of cultural production in ethnic minority media. In the context of the digital age, media are increasingly central as systems of representation of identity, culture and community. However, research examining how ethnic minority media become engaged in struggles of power is rare. Few works have paid attention to the ways in which race and gender operate in tandem to produce and maintain the unequal distribution of power in the mediascape of countries of post-colonial immigration. This paper juxtaposes gender studies and ethnic studies in order to analyse the representation of gender in ethnic media, with a particular focus on journalistic practices.     

The Danish cultural world of unbridgeable differences

This article looks at the contestation of foreign presence in Denmark from the perspective of popular consciousness. I infer the cultural world of Danish host and non-Danish guests from a pool of 55 in-depth interviews about multicultural issues. In this culturally figured world the guests are constructed as widely different cultural bearers who refuse to downplay their cultural markers, therefore upsetting the guests. According to this reasoning, the racial outburst of the hosts is caused solely by the unruly guests. Blaming the guests for creating racist responses, I contend, can best be understood as a naturalization of racism. This denial of racism in the popular sphere builds on the same culturalist construction of unbridgeable differences between a ‘we-group’ of ‘alike’ (or invisible) Danes and a visible ‘out group’ that dominates both popular and political understandings of immigrants and refugees in Denmark in the end of the 1990s.     

Cumulative cultural dynamics and the coevolution of cultural innovation and transmission: an ESS model for panmictic and structured populations

When individuals in a population can acquire traits through learning, each individual may express a certain number of distinct cultural traits. These traits may have been either invented by the individual himself or acquired from others in the population. Here, we develop a game theoretic model for the accumulation of cultural traits through individual and social learning. We explore how the rates of innovation, decay, and transmission of cultural traits affect the evolutionary stable (ES) levels of individual and social learning and the number of cultural traits expressed by an individual when cultural dynamics are at a steady‐state. We explore the evolution of these phenotypes in both panmictic and structured population settings. Our results suggest that in panmictic populations, the ES level of learning and number of traits tend to be independent of the social transmission rate of cultural traits and is mainly affected by the innovation and decay rates. By contrast, in structured populations, where interactions occur between relatives, the ES level of learning and the number of traits per individual can be increased (relative to the panmictic case) and may then markedly depend on the transmission rate of cultural traits. This suggests that kin selection may be one additional solution to Rogers's paradox of nonadaptive culture.     

Origins of life: a route to nanotechnology.

The origins of life and nanotechnology are two seemingly disparate areas of scientific investigation. However, the fundamental questions of life's beginnings and the applied construction of a Drexlerian nanotechnology both share a similar problem; how did and how can self-reproducing molecular machines originate? Here we draw attention to the coincidence between nanotechnology and origins research with particular attention paid to the spontaneous adsorption and scanning tunneling microscopy investigation of purine and pyrimidine bases self-organized into monolayers, adsorbed to the surfaces of crystalline solids. These molecules which encode biological information in nucleic acids, can form supramolecular architectures exhibiting enantiomorphism with the complexity to store and encode putative protobiological information. We conclude that the application of nanotechnology to the investigation of life's origins, and vice versa, could provide a viable route to an evolution-driven synthetic life.     

Naming taxa from cladograms: a cautionary tale

The recent publication of a new hypothesis of cladistic relationships among American frogs referred to the genus Rana, accompanied by a new taxonomy and a new nomenclature of this group [Hillis D.M., Wilcox, T.P., 2005. Phylogeny of the New World true frogs (Rana). Molecular Phylogenetics and Evolution 34, 299-314], draws attention to the problems posed by the use of a "double nomenclature", following both the rules of the International Code of Zoological Nomenclature (designated here as "onomatophore-based nomenclature") and the rules of the draft Phylocode (designated here as "definition-based nomenclature"). These two nomenclatural systems, which rely upon widely different theoretical bases, are incompatible, and the latter cannot be viewed as a "modification" of the former. Accordingly, scientific names (nomina) following both systems should be clearly distinguished in scientific publications. Onomatophore-based nomina should continue to be written as they have been for about 250 years, whereas definition-based nomina should be written in a specific way, e.g., Lithobates. The combined use of both nomenclatural systems for the same taxonomy in the same paper requires good knowledge and careful respect of the rules of the Code regarding availability, allocation and validity of nomina. As shown by this example, not doing so may result in various problems, in particular in publishing nomina nuda or in using nomenclatural ranks invalid under the current Code. Attention is drawn to the fact that new nomina published without diagnostic characters are not available under the Code, and that the latter currently forbids the use of more than two ranks (subgenus and "aggregate of species") between the ranks genus and species.     

Integrating an integrin: a direct route to actin

Integrins were so named for their ability to link the extracellular and intracellular skeletons. Now almost 20 years into integrin research, numerous questions remain as to how this interaction is accomplished and how it is modified to achieve a desired phenotype. As the cell adhesion and actin assembly fields are merging in combined approaches, novel actin assembly mechanisms are being uncovered. Some of the earliest identified cytoplasmic linker molecules, believed to mediate integrin-actin binding, are once again the subject of scrutiny as potential dynamic mediators of cell anchorage. It seems plausible that each unique cellular morphology occurs as the result of activation of distinct actin assembly systems that are either stabilized by unique bundling and linker proteins or modified for progression to a new phenotype. While this research initiative is likely to continue rapidly in a forward fashion, it remains to be clarified how integrins assemble the most stable and basic cytoskeletal phenotype, the adherent cell with prominent stress fibers. Recent investigations point towards a shift in the current model of anchoring at the cell periphery by providing both mechanisms and evidence for de novo actin assembly orchestrated by the adhesion site. Lacking a complete pathway from integrin ligation to an integrated extracellular-intracellular skeleton in any single system, this review proposes a simple model of integrin-mediated stress fiber integration by drawing from work in multiple systems.     

Protein mechanics: a route from structure to function

In order to better understand the mechanical properties of proteins, we have developed simulation tools which enable these properties to be analysed on a residue-by-residue basis. Although these calculations are relatively expensive with all-atom protein models, good results can be obtained much faster using coarse-grained approaches. The results show that proteins are surprisingly heterogeneous from a mechanical point of view and that functionally important residues often exhibit unusual mechanical behaviour. This finding offers a novel means for detecting functional sites and also potentially provides a route for understanding the links between structure and function in more general terms.     

Protein mechanics: a route from structure to function

In order to better understand the mechanical properties of proteins, we have developed simulation tools which enable these properties to be analysed on a residue-by-residue basis. Although these calculations are relatively expensive with all-atom protein models, good results can be obtained much faster using coarse-grained approaches. The results show that proteins are surprisingly heterogeneous from a mechanical point of view and that functionally important residues often exhibit unusual mechanical behaviour. This finding offers a novel means for detecting functional sites and also potentially provides a route for understanding the links between structure and function in more general terms.     

Minireview: Factors to Consider in the Naming of a G Protein-Coupled Receptor Subtype

Abstract

Receptors that mediate their effects through G proteins are predicted to have a seven transmembrane domain architecture. The last few years have seen a remarkable increase in the cloning of members of this superfamily leading to the identification of many more receptors than previously thought to exist on the basis of differences in agonist and antagonist specificities. This has important implications for nomenclature and classification, especially in view of the difficulty in relating receptors identified through cloning techniques to endogenously expressed receptors. Receptor cloning has also identified important differences in receptors between species raising the question as to whether these should be considered as species homologues or distinct subtypes. It is also becoming increasingly apparent that the pharmacology of this superfamily of receptors is influenced by the nature of the G protein present in the host cell and by alternative splicing of the receptor. The rapid pace of developments in this area necessitate the need for a regular publication summarizing recent developments. In the future, the cloning of G protein-coupled receptors will enable rationalization of the naming of individual receptor subtypes and identification of their inter-relationships.     

Endoderm development: from patterning to organogenesis

Although the ectoderm and mesoderm have been the focus of intensive work in the recent era of studies on the molecular control of vertebrate development, the endoderm has received less attention. Because signaling must occur between germ layers in order to achieve a properly organized body, our understanding of the coordinated development of all organs requires a more thorough consideration of the endoderm and its derivatives. This review focuses on present knowledge and perspectives concerning endoderm patterning and organogenesis. Some of the classical embryology of the endoderm is discussed and the progress and deficiencies in cellular and molecular studies are noted.     

Radical-radical reactions of superoxide: a potential route to toxicity

Superoxide reacts with many radicals, such as phenoxyl radicals, at near diffusion-controlled rates. These reactions are usually considered to be repair processes and have received little biological attention. However, addition of superoxide to give hydroperoxides and secondary oxidation products can also occur. The relative contributions of addition and repair vary depending on the properties of the phenol. With tyrosine, addition to give tyrosine hydroperoxide predominates, but in peptides the efficiency of hydroperoxide formation depends on the proximity of free amine groups. Radicals from other phenolic compounds, such as alpha-tocopherol and serotonin, also undergo addition reactions with superoxide. Physiologically, these reactions are likely to be more significant than dimerization when both radicals are generated together. They warrant attention as potential contributors to superoxide toxicity.