The ethics of ethical debates in peace and conflict research: Notes towards the development of a research covenant

This article outlines the case for peace and conflict researchers to formulate a research covenant to better shape their ethical obligations and responsibilities. This is an urgent necessity given that ethical debates have in some proponents become emotive and are not conducted in an ethical manner. In coming to this assessment, the article reviews trends in the research ethics literature and draws out some of the generic issues addressed in a review of the personal reflexivity that an assortment of individual peace and conflict researchers have engaged in when recounting their fieldwork experiences. These generic issues are reformulated in an attempt to codify appropriate ethical practice in peace and conflict research, and they go towards determining the contents of the research covenant. It is suggested that the research covenant is a more ethical way to debate the ethics of peace and conflict research.

Evolutionary diversification in Central Brazil: where Amazonia and Cerrado meet

Apesar da fauna de mamíferos Neotropicais ser uma das mais ricas do mundo, o nosso conhecimento sobre os limites de espécies, distribuições geográficas e relações filogenéticas está ainda agora no seu início. As áreas de transição entre os dois maiores biomas da América do Sul, o Cerrado e a Amazónia, são ainda menos conhecidas. Até ao momento, escassos estudos focaram os pequenos mamíferos destas áreas. Destes estudos, apenas dois apresentam dados taxonómicos e de distribuição geográfica de uma lista de espécies reduzida e, nenhum é focado nos processos evolutivos que conduziram à diversidade destas áreas. O presente trabalho tem como objectivo aumentar o conhecimento básico sobre a diversidade do médio Rio Araguaia, na região central do Brasil, através da amostragem e análise de espécies de pequenos mamíferos, integrando um intenso trabalho de campo, de laboratório e de museu. Desta forma, um total de 22 espécies é registado para o médio Araguaia. De entre estas espécies, descreve-se uma espécie nova de Rhipidomys, regista-se uma espécie não descrita de Thrichomys e uma potencial nova forma de Oligoryzomys, e também se apresenta uma diagnose emendada do obscuro Oecomys cleberi. Para cada espécie, são também descritas as suas características morfológicas e resumem-se os seus aspectos de distribuição geográfica e história natural. Para os quatro géneros acima referidos, são apresentadas as análises filogenéticas que permitem a identificação das espécies. Adicionalmente, os princípios da filogeografia são aplicados para estudar os padrões da distribuição geográfica da diversidade genética de três roedores sigmodontíneos e seis marsupiais didelphídeos. Os resultados obtidos demonstram que o Rio Araguaia forma uma barreira geográfica para espécies especialistas em florestas não-alagáveis; por outro lado, espécies generalistas apresentam partilha de haplótipos em ambas as margens do rio. Argumentamos também que os refúgios florestais e os gradientes poderão ter tido um papel importante para moldar a estrutura genética de populações de pequenos mamíferos no Brasil central. Em suma, os resultados apresentados corroboram a proposição de que a diversidade Neotropical não poderá ser explicada através de um único modelo de especiação e que estes não são mutuamente exclusivos. O entendimento integral dos processos ecológicos e históricos que deram origem à fauna Neotropical, assim como a continuidade de estudos sistemáticos, depende da realização de novas amostragens e consequente enriquecimento dos museus com colecções apropriadas.

Synthesis in the human evolutionary behavioural sciences

Over the last three decades, the application of evolutionary theory to the human sciences has shown remarkable growth. This growth has also been characterised by a ‘splitting’ process, with the emergence of distinct sub-disciplines, most notably: Human Behavioural Ecology (HBE), Evolutionary Psychology (EP) and studies of Cultural Evolution (CE). Multiple applications of evolutionary ideas to the human sciences are undoubtedly a good thing, demonstrating the usefulness of this approach to human affairs. However, this fracture has been associated with considerable tension, a lack of integration, and sometimes outright conflict between researchers. In recent years however, there have been clear signs of hope that a synthesis of the human evolutionary behavioural sciences is underway. Here, we briefly review the history of the debate, both its theoretical and practical causes; then provide evidence that the field is currently becoming more integrated, as the traditional boundaries between sub-disciplines become blurred. This article constitutes the first paper under the new editorship of the Journal of Evolutionary Psychology, which aims to further this integration by explicitly providing a forum for integrated work.

Fuzzy model identification by evolutionary, gradient based and memtic algorithms

One of the crucial problems of fuzzy rule modeling is how to find an optimal or at least a quasi-optimal rule base fro a certain system. In most applications there is no human expert available, or, the result of a human expert's decision is too much subjective and is not reproducible, thus some automatic method to determine the fuzzy rule base must be deployed.

Design of neuro-fuzzy models by evolutionary and gradient-based algorithms

All systems found in nature exhibit, with different degrees, a nonlinear behavior. To emulate this behavior, classical systems identification techniques use, typically, linear models, for mathematical simplicity. Models inspired by biological principles (artificial neural networks) and linguistically motivated (fuzzy systems), due to their universal approximation property, are becoming alternatives to classical mathematical models. In systems identification, the design of this type of models is an iterative process, requiring, among other steps, the need to identify the model structure, as well as the estimation of the model parameters. This thesis addresses the applicability of gradient-basis algorithms for the parameter estimation phase, and the use of evolutionary algorithms for model structure selection, for the design of neuro-fuzzy systems, i.e., models that offer the transparency property found in fuzzy systems, but use, for their design, algorithms introduced in the context of neural networks. A new methodology, based on the minimization of the integral of the error, and exploiting the parameter separability property typically found in neuro-fuzzy systems, is proposed for parameter estimation. A recent evolutionary technique (bacterial algorithms), based on the natural phenomenon of microbial evolution, is combined with genetic programming, and the resulting algorithm, bacterial programming, advocated for structure determination. Different versions of this evolutionary technique are combined with gradient-based algorithms, solving problems found in fuzzy and neuro-fuzzy design, namely incorporation of a-priori knowledge, gradient algorithms initialization and model complexity reduction.

Cloning of the Bone Gla Protein gene from the teleost fish Sparus aurata (gilthead seabream). Molecular organization, developmental appearance and evolutionary implications

Tese de Doutoramento, Biologia Molecular, Faculdade de Ciências do Mar e do Ambiente, Universidade do Algarve, 2001

Environmental ethics: philosophy, ecology and other species

Pressure on the environment has increased in step with economic growth and the mass consumption that fueled rising gross domestic product throughout the twentieth century. Both growth and ecological crises have attained a global reach, challenging our established notions of cause and effect, and our framing of problems and solutions. Accordingly, global environmental politics has witnessed major changes and significant "rescaling" in its "locus, agency and scope" (Andonova and Mitchell2010: 257). Both dimensions of global environmental politics - politics and governance, and the ecological problems that are the subject matter of global environmental politics - are being reinterpreted due to increasing complexity, interconnectedness and interdependence. Accordingly, the range of actors and disciplines that infom1 global environmental politics and contribute to framing global environmental problems is widening, in an acknowledgment of inescapable pluralism.

The metamorphosis of authority: a case study of the Aga Khan Development Network and the Ismaili Imamate

This research is a study of modern developments of the institutions of the Nizārī Ismaili imamate during the time of the present Ismaili Imam, Shāh Karīm al-Ḥusaynī, Aga Khan IV, as the 49th hereditary living Imam of Shiʿi Nizārī Ismaili Muslims, particularly addressing the formation of the Aga Khan Development Network (AKDN) and the functions of the Community institutions. Using the case study of the Aga Khan Development Network and the Nizārī Ismaili imamate, this research demonstrates that the three ideal types of authority as proposed by Weber, namely the traditional, charismatic and legal-bureaucratic types, are not sufficient to explain the dynamics of authority among Muslims. This is partly due to Weber’s belief in the uniqueness of Western civilisation, which is a product of his thesis on Protestant Ethics and partly because his ideal typical system does not work in the case of the Muslim societies. The Ismaili imamate with its multifarious institutions in contemporary times is the most suitable counter-example by which to powerfully demonstrate that Weberian models of authority fail to explain this phenomenon and it would indeed appear as a paradoxical institution if viewed with Weberian theses. The Ismaili imamate in contemporary times represents a paradigm shift and a transmutation not only as regards the Weberian models but also when viewed from inside the tradition of Shiʿi Muslim history. This evolutionary leap forward, which has been crystallised over the course of the past half a century, in the Ismaili imamate suggests the development of a new form of authority which is unprecedented. There are clearly various elements in this form of authority which could be discerned as rooted in tradition and history; however the distinctive elements of this new form of authority give it a defining and exciting dimension. There are several qualities which are peculiar to the contemporary condition of the Ismaili imamate and its style of leadership which are distinctive. Most importantly, while some central features, like succession by way of designation (naṣṣ) has not changed, there is one overarching quality which can best capture all these elements and that is the transmutation of the Ismaili imamate from the person of the Imam into the office of imamate and thus we are now facing the institutionalisation of the imamate and the office being the embodiment of the authority of the Imam. I have described this new development as a metamorphosis of the authority because it gives an entirely new form and content to the previously familiar concept of authority in the Shiʿi Ismaili Muslim tradition.

Intersubjectivity and a practical intersubjective ethics of translation

This essay suggests that the intersubjectivity in translation should be given priority because different stages of the translation activity have different subjects, and presents a practical intersubjective ethics of translation based on an interpretation of the intersubjective relations connected with translation activities in a perspective of game theory in the hope that it can equip us with better explanations of the translator’s calculations or considerations in the professional practice.

Evolutionary trajectory optimization for redundant robots

The trajectory planning of redundant robots is an important area of research and efficient optimization algorithms have been investigated in the last years. This paper presents a new technique that combines the closed-loop pseudoinverse method with genetic algorithms. In this case the trajectory planning is formulated as an optimization problem with constraints.

Music and evolutionary computation

This paper presents a brief history of the western music: from its genesis to serialism and the Darmstadt school. Also some mathematical aspects of music are then presented and confronted with music as a form of art. The question is, are these two distinct aspects compatible? Can computers be of real help in automatic composition? The more appealing algorithmic approach is evolutionary computation as it offers creativity potential. Therefore, the Evolutionary Algorithms are then introduced and some results of GAs and GPs application to music generation are analysed.

An evolutionary approach for the motion planning of redundant and hyper-redundant manipulators

The trajectory planning of redundant robots is an important area of research and efficient optimization algorithms are needed. The pseudoinverse control is not repeatable, causing drift in joint space which is undesirable for physical control. This paper presents a new technique that combines the closed-loop pseudoinverse method with genetic algorithms, leading to an optimization criterion for repeatable control of redundant manipulators, and avoiding the joint angle drift problem. Computer simulations performed based on redundant and hyper-redundant planar manipulators show that, when the end-effector traces a closed path in the workspace, the robot returns to its initial configuration. The solution is repeatable for a workspace with and without obstacles in the sense that, after executing several cycles, the initial and final states of the manipulator are very close.

An integrated approach to Physcomitrella patens transcriptomics reveals importantclues of the evolutionary development of plant organs and sexual reproduction

Land plant evolution required the generation of a new body plan that could resist the harsher and fluctuating environmental conditions found outside of aquatic environments. Unraveling the genetic basis of plant developmental innovations is not only revealing in terms of an evolutionary point of view, but it is also important for understanding the emergence of agronomically important traits. Comparative genetic studies between basal and modern land plants, both at the genome and trancriptome levels, can help in the generation of hypotheses related to the genetic basis of plant evolutionary development.(...)

Evolutionary dynamics of Chlamydia trachomatis genome and identification of molecular patterns of hypothetical protein coding genes

The obligate intracellular bacterium Chlamydia trachomatis is a human pathogen of major public health significance. Strains can be classified into 15 main serovars (A to L3) that preferentially cause ocular infections (A-C), genital infections (D-K) or lymphogranuloma venereum (LGV) (L1-L3), but the molecular basis behind their distinct tropism, ecological success and pathogenicity is not welldefined. Most chlamydial research demands culture in eukaryotic cell lines, but it is not known if stains become laboratory adapted. By essentially using genomics and transcriptomics, we aimed to investigate the evolutionary patterns underlying the adaptation of C. trachomatis to the different human tissues, given emphasis to the identification of molecular patterns of genes encoding hypothetical proteins, and to understand the adaptive process behind the C. trachomatis in vivo to in vitro transition. Our results highlight a positive selection-driven evolution of C. trachomatis towards nichespecific adaptation, essentially targeting host-interacting proteins, namely effectors and inclusion membrane proteins, where some of them also displayed niche-specific expression patterns. We also identified potential "ocular-specific" pseudogenes, and pointed out the major gene targets of adaptive mutations associated with LGV infections. We further observed that the in vivo-derived genetic makeup of C. trachomatis is not significantly compromised by its long-term laboratory propagation. In opposition, its introduction in vitro has the potential to affect the phenotype, likely yielding virulence attenuation. In fact, we observed a "genital-specific" rampant inactivation of the virulence gene CT135, which may impact the interpretation of data derived from studies requiring culture. Globally, the findings presented in this Ph.D. thesis contribute for the understanding of C.trachomatis adaptive evolution and provides new insights into the biological role of C. trachomatishypothetical proteins. They also launch research questions for future functional studies aiming toclarify the determinants of tissue tropism, virulence or pathogenic dissimilarities among C. trachomatisstrains.