PICES Press, Vol. 20, No. 1, Winter 2012

•2011 PICES Science: A Note from the Science Board Chairman (pp. 1-6) •2011 PICES Awards (pp. 7-9) •Beyond the Terrible Disaster of the Great East Japan Earthquake (pp. 10-12) •A New Era of PICES-ICES Scientific Cooperation (p. 13) •New PICES Jellyfish Working Group Formed (pp. 14-15) •PICES Working Group on North Pacific Climate Variability (pp. 16-18) •Final U.S. GLOBEC Symposium and Celebration (pp. 19-25) •2011 PICES Rapid Assessment Survey (pp. 26-29) •Introduction to Rapid Assessment Survey Methodologies for Detecting Non-indigenous Marine Species (pp. 30-31) •The 7th International Conference on Marine Bioinvasions (pp. 32-33) •NOWPAP/PICES/WESTPAC Training Course on Remote Sensing Data Analysis (pp. 34-36) •PICES-2011 Workshop on “Trends in Marine Contaminants and their Effects in a Changing Ocean” (pp. 37-39) •The State of the Western North Pacific in the First Half of 2011 (pp. 40-42) •Yeosu Symposium theme sessions (p. 42) •The Bering Sea: Current Status and Recent Events (pp. 43-44) •News of the Northeast Pacific Ocean (pp. 45-47) •Recent and Upcoming PICES Publications (p. 47) •New leadership for the PICES Fishery Science Committee (p. 48

Upright posture and the meaning of meronymy: A synthesis of metaphoric and analytic accounts

Cross-linguistic strategies for mapping lexical and spatial relations from body partonym systems to external object meronymies (as in English ‘table leg’, ‘mountain face’) have attracted substantial research and debate over the past three decades. Due to the systematic mappings, lexical productivity and geometric complexities of body-based meronymies found in many Mesoamerican languages, the region has become focal for these discussions, prominently including contrastive accounts of the phenomenon in Zapotec and Tzeltal, leading researchers to question whether such systems should be explained as global metaphorical mappings from bodily source to target holonym or as vector mappings of shape and axis generated “algorithmically”. I propose a synthesis of these accounts in this paper by drawing on the species-specific cognitive affordances of human upright posture grounded in the reorganization of the anatomical planes, with a special emphasis on antisymmetrical relations that emerge between arm-leg and face-groin antinomies cross-culturally. Whereas Levinson argues that the internal geometry of objects “stripped of their bodily associations” (1994: 821) is sufficient to account for Tzeltal meronymy, making metaphorical explanations entirely unnecessary, I propose a more powerful, elegant explanation of Tzeltal meronymic mapping that affirms both the geometric-analytic and the global-metaphorical nature of Tzeltal meaning construal. I do this by demonstrating that the “algorithm” in question arises from the phenomenology of movement and correlative body memories—an experiential ground which generates a culturally selected pair of inverse contrastive paradigm sets with marked and unmarked membership emerging antithetically relative to the transverse anatomical plane. These relations are then selected diagrammatically for the classification of object orientations according to systematic geometric iconicities. Results not only serve to clarify the case in question but also point to the relatively untapped potential that upright posture holds for theorizing the emergence of human cognition, highlighting in the process the nature, origins and theoretical validity of markedness and double scope conceptual integration

Embodied Robot Models for Interdisciplinary Emotion Research

Due to their complex nature, emotions cannot be properly understood from the perspective of a single discipline. In this paper, I discuss how the use of robots as models is beneficial for interdisciplinary emotion research. Addressing this issue through the lens of my own research, I focus on a critical analysis of embodied robots models of different aspects of emotion, relate them to theories in psychology and neuroscience, and provide representative examples. I discuss concrete ways in which embodied robot models can be used to carry out interdisciplinary emotion research, assessing their contributions: as hypothetical models, and as operational models of specific emotional phenomena, of general emotion principles, and of specific emotion ``dimensions''. I conclude by discussing the advantages of using embodied robot models over other models.Peer reviewe

Coupling metabolic footprinting and flux balance analysis to predict how single gene knockouts perturb microbial metabolism

Tese de mestrado. Biologia (Bioinformática e Biologia Computacional). Universidade de Lisboa, Faculdade de Ciências, 2012The model organisms Caenorhabditis elegans and E. coli form one of the simplest gut microbe host interaction models. Interventions in the microbe that increase the host longevity including inhibition of folate synthesis have been reported previously. To find novel single gene knockouts with an effect on lifespan, a screen of the Keio collection of E. coli was undertaken, and some of the genes found are directly involved in metabolism. The next step in those specific cases is to understand how these mutations perturb metabolism systematically, so that hypotheses can be generated. For that, I employed dynamic Flux Balance Analysis (dFBA), a constraint-based modeling technique capable of simulating the dynamics of metabolism in a batch culture and making predictions about changes in intracellular flux distribution. Since the specificities of the C. elegans lifespan experiments demand us to culture microbes in conditions differing from most of the published literature on E. coli physiology, novel data must be acquired to characterize and make dFBA simulations as realistic as possible. To do this exchange fluxes were measured using quantitative H NMR Time-Resolved Metabolic Footprinting. Furthermore, I also investigate the combination of TReF and dFBA as a tool in microbial metabolism studies. These approaches were tested by comparing wild type E. coli with one of the knockout strains found, ΔmetL, a knockout of the metL gene which encodes a byfunctional enzyme involved in aspartate and threonine metabolism. I found that the strain exhibits a slower growth rate than the wild type. Model simulation results revealed that reduced homoserine and methionine synthesis, as well as impaired sulfur and folate metabolism are the main effects of this knockout and the reasons for the growth deficiency. These results indicate that there are common mechanisms of the lifespan extension between ΔmetL and inhibition of folate biosynthesis and that the flux balance analysis/metabolic footprinting approach can help us understand the nature of these mechanisms.Os organismos modelo Caenorhabditis elegans e E. coli formam um dos modelos mais simples de interacções entre micróbio do tracto digestivo e hospedeiro. Intervenções no micróbio capazes de aumentar a longevidade do hospedeiro, incluindo inibição de síntese de folatos, foram reportadas previamente. Para encontrar novas delecções génicas do micróbio capazes de aumentar a longevidade do hospedeiro, a colecção Keio de deleções génicas de E. coli foi rastreada. Alguns dos genes encontrados participam em processos metabólicos, e nesses casos, o próximpo passo é perceber como as deleções perturbam o metabolismo sistémicamente, para gerar hipóteses. Para isso, utilizo dynamic Flux Balance Analysis (dFBA), uma técnica de modelação metabólica capaz de fazer previsões sobre alterações na distribuição intracelular de fluxos. As especificidades das experiências de tempo de vida em C.elegans obrigam-nos a trabalhar em condições diferentes das usadas na maioria da literatura publicada em fisiologia de E. coli, e para dar o máximo realismo às simulações de dFBA novos dados foram adquiridos, utilizando H NMR Time-Resolved Metabolic Footprinting para medir fluxos de troca de metabolitos entre microorganismo e meio de cultura. A combinação de TReF e dFBA como ferramenta de estudo do metabolism microbiano é também investigada. Estas abordagens foram testadas ao comparar E. coli wild-type com uma das estirpes encontradas no rastreio, ΔmetL, knockout do gene metL, que codifica um enzima bifunctional participante no metabolismo de aspartato e treonina, e que exibe uma taxa de crescimento reduzida comparativamente ao wild-type. Os resultados das simulações revelaram que os principais efeitos da deleção deste gene, e as razões para a menor taxa de crescimento observada, são a produção reduzida de homoserina e metionina e os efeitos que provoca no metabolismo de folatos e enxofre. Estes resultados indicam que há mecanismos comuns na extensão da longevidade causada por esta deleção e inibição de síntese de folatos, e que a combinação metabolic footprinting/flux balance analysis pode ajudar-nos a compreender a natureza desses mecanismos

Effects of Roads and Traffic on Wildlife Populations and Landscape Function Road Ecology is Moving toward Larger Scales

Road ecology has developed into a significant branch of ecology with steady growth in the number of refereed journal articles, books, conferences, symposia, and “best practice” guidelines being produced each year. The main objective of this special issue of Ecology and Society is to highlight the need for studies that document the population, community, and ecosystem-level effects of roads and traffic by publishing studies that document these effects. It became apparent when compiling this special issue that there is a paucity of studies that explicitly examined higher order effects of roads and traffic. No papers on landscape function or ecosystem-level effects were submitted, despite being highlighted as a priority for publication. The 17 papers in this issue, from Australia, Canada, the Netherlands, and USA, all deal to some extent with either population or community-level effects of roads and traffic. Nevertheless, many higher order effects remain unquantified, and must become the focus of future studies because the complexity and interactions among the effects of roads and traffic are large and potentially unexpected. An analysis of these complex interrelations requires systematic research, and it is necessary to further establish collaborative links between ecologists and transportation agencies. Many road agencies have “environmental sustainability” as one of their goals and the only way to achieve such goals is for them to support and foster long-term and credible scientific research. The current situation, with numerous small-scale projects being undertaken independently of each other, cannot provide the information required to quantify and mitigate the negative effects of roads and traffic on higher levels. The future of road ecology research will be best enhanced when multiple road projects in different states or countries are combined and studied as part of integrated, well-replicated research projects

Objectivity: its meaning, its limitations, its fateful omissions

In this text, we explore the guiding thread of the volume "Objectivity after Kant" by first discussing how the main question pertaining to transcendental objectivity arose at the Centre for Critical Philosophy. This exposition takes the form of a microhistorical genealogy, from which the main ideas pursued in the research conducted at this Centre can be distilled. In the second part, we briefly sketch how the different contributors have addressed this question. Its purpose is to facilitate the reader’s navigation through the variety of topics and perspectives addressed throughout this volume, and incite further reflection on the central issue it pursues

PICES Press, Vol. 19, No. 1, Winter 2011

•2010 PICES Science: A Note from the Former Science Board Chairman (pp. 1-4) •2010 PICES Awards (pp. 5-7) •The First Year of FUTURE: A Progress Report (pp. 8-13) •New Chairmen in PICES (pp. 14-19) •Pacific Ocean Interior Carbon Data Synthesis, PACIFICA, in Progress (pp. 20-23) •2011 PICES Calendar (p. 23) •Ecosystems 2010: Global Progress on Ecosystem-based Fisheries Management (pp. 24-26) •PICES 2010 Rapid Assessment Survey (pp. 27-29) •PICES Workshop on “An Introduction to Rapid Assessment Survey Methodologies for Application in Developing Countries” (pp. 30-31) •The State of the Western North Pacific in the First Half of 2010 (pp. 32-34) •PICES Interns (p. 34) •The State of the Bering Sea in 2010 (pp. 35-37) •The State of the Northeast Pacific in 2010 (pp. 38-40