Periodic Reordering

For many networks in nature, science and technology, it is possible to order the nodes so that most links are short-range, connecting near-neighbours, and relatively few long-range links, or shortcuts, are present. Given a network as a set of observed links (interactions), the task of finding an ordering of the nodes that reveals such a range-dependent structure is closely related to some sparse matrix reordering problems arising in scientific computation. The spectral, or Fiedler vector, approach for sparse matrix reordering has successfully been applied to biological data sets, revealing useful structures and subpatterns. In this work we argue that a periodic analogue of the standard reordering task is also highly relevant. Here, rather than encouraging nonzeros only to lie close to the diagonal of a suitably ordered adjacency matrix, we also allow them to inhabit the off-diagonal corners. Indeed, for the classic small-world model of Watts & Strogatz (1998, Collective dynamics of ‘small-world’ networks. Nature, 393, 440–442) this type of periodic structure is inherent. We therefore devise and test a new spectral algorithm for periodic reordering. By generalizing the range-dependent random graph class of Grindrod (2002, Range-dependent random graphs and their application to modeling large small-world proteome datasets. Phys. Rev. E, 66, 066702-1–066702-7) to the periodic case, we can also construct a computable likelihood ratio that suggests whether a given network is inherently linear or periodic. Tests on synthetic data show that the new algorithm can detect periodic structure, even in the presence of noise. Further experiments on real biological data sets then show that some networks are better regarded as periodic than linear. Hence, we find both qualitative (reordered networks plots) and quantitative (likelihood ratios) evidence of periodicity in biological networks.

Interactions between earthworms and arsenic in the soil environment: a review

Chemical pollution of the environment has become a major source of concern. In particular, many studies have investigated the impact of pollution on biota in the environment. Studies on metalliferous contaminated mine spoil wastes have shown that some soil organisms have the capability to become resistant to metal/metalloid toxicity. Earthworms are known to inhabit arsenic-rich metalliferous soils and, due to their intimate contact with the soil, in both the solid and aqueous phases, are likely to accumulate contaminants present in mine spoil. Earthworms that inhabit metalliferous contaminated soils must have developed mechanisms of resistance to the toxins found in these soils. The mechanisms of resistance are not fully understood; they may involve physiological adaptation (acclimation) or be genetic. This review discusses the relationships between earthworms and arsenic-rich mine spoil wastes, looking critically at resistance and possible mechanisms of resistance, in relation to soil edaphic factors and possible trophic transfer routes. (C) 2003 Elsevier Science Ltd. All rights reserved.

Macroevolutionary patterns in the origin of mutualisms involving ants

Ants are a diverse and abundant insect group that form mutualistic associations with a number of different organisms from fungi to insects and plants. Here, we use a phylogenetic approach to identify ecological factors that explain macroevolutionary trends in the mutualism between ants and honeydew-producing Homoptera. We also consider association between ant-Homoptera, ant-fungi and ant-plant mutualisms. Homoptera-tending ants are more likely to be forest dwelling, polygynous, ecologically dominant and arboreal nesting with large colonies of 10(4)-10(5) individuals. Mutualistic ants (including those that garden fungi and inhabit ant-plants) are found in under half of the formicid subfamilies. At the genus level, however, we find a negative association between ant-Homoptera and ant-fungi mutualisms, whereas there is a positive association between ant-Homoptera and ant-plant mutualisms. We suggest that species can only specialize in multiple mutualisms simultaneously when there is no trade-off in requirements from the different partners and no redundancy of rewards.

Influence of occupant microhabitat on the composition of encrusting communities on gastropod shells

The exploitation of microhabitats is widely considered to increase biodiversity in marine ecosystems. Although intertidal hermit crabs and gastropods may inhabit the same shell type and shore level, their microhabitat may differ depending on the state of the tide. On the south coast of Wales the hermit crab Pagurus bernhardus mainly inhabits the shells of Nucella lapillus (84%). Hermit crab shells had a significantly different encrusting community compared with live N. lapillus shells. At low tide the live gastropods were found on exposed rock surfaces whereas hermit crabs were restricted to tidal pools. Communities encrusting live gastropod shells were characterised by lower species richness and abundance compared with shells inhabited by hermit crabs (12 species found in total). A greater abundance and richness of epibionts was recorded from both shell types during the summer compared with winter. Differences in community composition between shell occupant types were attributed to microhabitats used by gastropods and hermit crabs and the associated desiccation pressures, rather than competitive interactions or shell characteristics. This contradicts earlier studies of subtidal shells where biological processes were considered more important than physical factors in controlling species abundance and richness patterns. The use of rockpool microhabitats by hermit crabs increases the biodiversity of rocky shores, as some species commonly found on hermit-crab-inhabited shells were rare in other local habitats.

Habitat correlates of distribution and local population decline of the endemic Sardinian newt Euproctus platycephalus

Habitat-based statistical models relating patterns of presence and absence of species to habitat variables could be useful to resolve conservation-related problems and highlight the causes of population declines. In this paper, we apply such a modelling approach to an endemic amphibian, the Sardinian mountain newt Euproctus platycephalus, considered by IUCN a critically endangered species. Sardinian newts inhabit freshwater habitat in streams, small lakes and pools on the island of Sardinia (Italy). Reported declines of newt populations are not yet supported by quantitative data, however, they are perceived or suspected across the species' historical range. This study represents a first attempt trying to statistically relate habitat characteristics to Sardinian newt occurrence and persistence. Linear regression analysis revealed that newts are more likely to be found in sites with colder water temperature, less riparian vegetation and, marginally, absence of fish. The implications of the results for the conservation of the species are discussed, and suggestions for the short-term management of newt inhabited sites suggested. (C) 2003 Elsevier Ltd. All rights reserved.

Island ecosystems - priorities for conservation?

In terms of their land area, many islands contain a disproportionate number of taxa for certain groups of organisms. Thus the IUCN/WWF Centres of Plant Diversity project, which identifies 234 first order sites that are globally most important from a botanical point of view, includes a considerable proportion of islands, and in Conservation International’s Hotspot programme, Madagascar and the Indian Ocean Islands, the Philippines, and the Caribbean are identified as three of the five “hottest of the hotspots”. Priority for conservation action is often assumed for islands because of the often dramatic losses already suffered and the serious level of threats to which plant or animal populations are subjected, largely as a result of direct or indirect human action. The practicalities of conservation are not, however, straightforward in many cases. In the conservation of island hotspots of biodiversity, in addition to the many scientific and technical issues involved, political, financial and socio-economic factors also have to be addressed. The priorities for conservation will be examined in the light of targets set by the recently approved CBD Global Strategy for Plant Conservation and in the wider context of sustainable development of island ecosystems and the needs and aspirations of the people who inhabit them. Particular attention will be given to the threats from invasive species and the resultant increasing homogenization of floras and faunas, leading to the ‘deinsularization’ of islands.

A naked ape would have fewer parasites

Unusually among the mammals, humans lack an outer layer of protective fur or hair. We propose the hypothesis that humans evolved hairlessness to reduce parasite loads, especially ectoparasites that may carry disease. We suggest that hairlessness is maintained by these naturally selected benefits and by sexual selection operating on both sexes. Hairlessness is made possible in humans owing to their unique abilities to regulate their environment via fire, shelter and clothing. Clothes and shelters allow a more flexible response to the external environment than a permanent layer of fur and can be changed or cleaned if infested with parasites. Naked mole-rats, another hairless and non-aquatic mammal species, also inhabit environments in which ectoparasite transmission is expected to be high, but in which temperatures are closely regulated. Our hypothesis explains features of human hairlessness-such as the marked sex difference in body hair, and its retention in the pubic regions-that are not explained by other theories.

Knowing who likes who: The early developmental basis of coalition understanding

Group biases based on broad category membership appear early in human development. However, like many other primates humans inhabit social worlds also characterised by small groups of social coalitions which are not demarcated by visible signs or social markers. A critical cognitive challenge for a young child is thus how to extract information concerning coalition structure when coalitions are dynamic and may lack stable and outwardly visible cues to membership. Therefore, the ability to decode behavioural cues of affiliations present in everyday social interactions between individuals would have conferred powerful selective advantages during our evolution. This would suggest that such an ability may emerge early in life, however, little research has investigated the developmental origins of such processing. The present paper will review recent empirical research which indicates that in the first 2 years of life infants achieve a host of social-cognitive abilities that make them well adapted to processing coalition-affiliations of others. We suggest that such an approach can be applied to better understand the origins of intergroup attitudes and biases. Copyright © 2010 John Wiley & Sons, Ltd.

Robot free will

We introduce the perspex machine which unifies projective geometry and Turing computation and results in a supra-Turing machine. We show two ways in which the perspex machine unifies symbolic and non-symbolic AI. Firstly, we describe concrete geometrical models that map perspexes onto neural networks, some of which perform only symbolic operations. Secondly, we describe an abstract continuum of perspex logics that includes both symbolic logics and a new class of continuous logics. We argue that an axiom in symbolic logic can be the conclusion of a perspex theorem. That is, the atoms of symbolic logic can be the conclusions of sub-atomic theorems. We argue that perspex space can be mapped onto the spacetime of the universe we inhabit. This allows us to discuss how a robot might be conscious, feel, and have free will in a deterministic, or semi-deterministic, universe. We ground the reality of our universe in existence. On a theistic point, we argue that preordination and free will are compatible. On a theological point, we argue that it is not heretical for us to give robots free will. Finally, we give a pragmatic warning as to the double-edged risks of creating robots that do, or alternatively do not, have free will.

Pseudomonas genomes: diverse and adaptable

Members of the genus Pseudomonas inhabit a wide variety of environments, which is reflected in their versatile metabolic capacity and broad potential for adaptation to fluctuating environmental conditions. Here, we examine and compare the genomes of a range of Pseudomonas spp. encompassing plant, insect and human pathogens, and environmental saprophytes. In addition to a large number of allelic differences of common genes that confer regulatory and metabolic flexibility, genome analysis suggests that many other factors contribute to the diversity and adaptability of Pseudomonas spp. Horizontal gene transfer has impacted the capability of pathogenic Pseudomonas spp. in terms of disease severity (Pseudomonas aeruginosa) and specificity (Pseudomonas syringae). Genome rearrangements likely contribute to adaptation, and a considerable complement of unique genes undoubtedly contributes to strain- and species-specific activities by as yet unknown mechanisms. Because of the lack of conserved phenotypic differences, the classification of the genus has long been contentious. DNA hybridization and genome-based analyses show close relationships among members of P. aeruginosa, but that isolates within the Pseudomonas fluorescens and P. syringae species are less closely related and may constitute different species. Collectively, genome sequences of Pseudomonas spp. have provided insights into pathogenesis and the genetic basis for diversity and adaptation.

Svetlana

Svetlana is a series of photographs documenting rehearsals for an opera that was never performed. Written by Waw Pierogi, founder of the 1980s group Xex, little is known of the opera, only that it was inspired by Svetlana, a character from one of their songs and the daughter of Stalin, who defected from the Soviet Union twice. A fictional Svetlana and a bogus Leon Theremin - inventor of the eponymous hands-free electronic musical instrument who was later kidnapped by the KGB - inhabit an archive of photographs from a session of stage rehearsals and location shots. Combining Svetlana’s narrative with a conspiracy to create sound weapons, this documentation of theatre workshops, styled after Bauhaus drama class exercises, produces an entirely spurious story of espionage, sonic weaponry and the clash between love and ideology. The performers sport geometric military costumes, brandishing sculptural forms fashioned after the acoustic locators that preceded radar technology. These redundant locators were still kept in use as props, concealing the introduction of radar from the Germans. They perfectly capture the theatricality of military might and suggest the rhetorical force of sound or even the political power of art. Svetlana was originally produced as part of a residency at S1 Artspace, Sheffield, and was later shown at Tatty Devine, alongside a special capsule collection of jewellery made by Tatty Devine.

The embodied use of the material home: an affordance approach

This paper examines the relationship between embodied individuals and the home that they inhabit. Although there has been some work on both the embodied practices in the home and on the material nature of the home itself, this has not been integrated with the majority of research on home which has focused on meaning. It is argued that there is a lack of a unifying framework that can incorporate both use and meaning elements of home. A way of incorporating these elements through adoption of the concept of affordances is put forward. However, the affordance approach needs to be developed to achieve this. The paper does this first by incorporating the concept of intentionality of actions and then through the use of the concept of well‐being. Debates about housing for people with a physical disability and the practical help provided to this group of people are used to illustrate how the approach could work.

Thorn-dwelling ants provide antiherbivore defence for camelthorn trees, Vachellia erioloba, in Namibia

Ants are widely employed by plants as an antiherbivore defence. A single host plant can associate with multiple, symbiotic ant species, although usually only a single ant species at a time. Different plant-ant species may vary in the degree to which they defend their host plant. In Kenya, ant–acacia interactions are well studied, but less is known about systems elsewhere in Africa. A southern African species, Vachellia erioloba, is occupied by thorn-dwelling ants from three different genera. Unusually, multiple colonies of all these ants simultaneously and stably inhabit trees. We investigated if the ants on V. erioloba (i) deter insect herbivores; (ii) differ in their effectiveness depending on the identity of the herbivore; and (iii) protect the tree against an important herbivore, the larvae of the lepidopteran Gonometa postica. We show that experimental exclusion of ants leads to greater levels of herbivory on trees. The ants inhabiting V. erioloba are an effective deterrent against hemipteran and coleopteran, but not lepidopteran herbivores. Defensive services do not vary among ant species, but only Crematogaster ants exhibit aggression towards G. postica. This highlights the potential of the V. erioloba–ant mutualism for studying ant–plant interactions that involve multiple, simultaneously resident thorn-dwelling ant species.

Cultural phylogeography of the Bantu Languages of sub-Saharan Africa

There is disagreement about the routes taken by populations speaking Bantu languages as they expanded to cover much of sub-Saharan Africa. Here, we build phylogenetic trees of Bantu languages and map them onto geographical space in order to assess the likely pathway of expansion and test between dispersal scenarios. The results clearly support a scenario in which groups first moved south through the rainforest from a homeland somewhere near the Nigeria–Cameroon border. Emerging on the south side of the rainforest, one branch moved south and west. Another branch moved towards the Great Lakes, eventually giving rise to the monophyletic clade of East Bantu languages that inhabit East and Southeastern Africa. These phylogenies also reveal information about more general processes involved in the diversification of human populations into distinct ethnolinguistic groups. Our study reveals that Bantu languages show a latitudinal gradient in covering greater areas with increasing distance from the equator. Analyses suggest that this pattern reflects a true ecological relationship rather than merely being an artefact of shared history. The study shows how a phylogeographic approach can address questions relating to the specific histories of certain groups, as well as general cultural evolutionary processes.

Spiral jetty, thirty seven years later: the cinematic time of James Benning

This article considers cinematic time in James Benning’s film, casting a glance (2007), in relation to its subject, Robert Smithson’s 1970 earthwork Spiral Jetty, and his film of the same name. The radicalism of Smithson’s thinking on time has been widely acknowledged, and his influence continues to pervade contemporary artistic practice. The relationship of Benning’s films with this legacy may appear somewhat oblique, given their apparent phenomenological rendition of ‘real time’. However, closer examination of Benning’s formal strategies reveals a more complex temporal construction, characterized by uncertain intervals that interrupt the folding of cinematic time into the flow of consciousness. Smithson’s film uses cinematic analogy to gesture towards vast reaches of geological time; Benning’s film creates a simulated timescale to evoke the short history of the earthwork itself. Smithson’s embrace of the entropic was a counter-cultural stance at the end of the1960s, but under the shadow of ecological disaster, this orientation has come to appear melancholy and romantic rather than radical. Benning’s film returns the jetty to anthropic time, but raises questions about the ways we inhabit time. His practice of working with ‘borrowed time’ is particularly suited to the cultural and historical moment of his later work.