Ecosystem health and malfunctions: an organisational perspective.

A recent idea of "ecosystem health" was introduced in the 1970s and 1980s to draws attention to the fact that ecosystems can become ill because of a reduction of properties such as primary productivity, functions and diversity of interactions among system components. Starting from the 1990s, this idea has been deeply criticized by authors who argued that, insofar as ecosystems show many differences with respect to organismic features, these two kinds of systems cannot share a typical organismic property such as health. In recent years, an organisational approach in philosophy of biology and ecology argued that both organisms and ecosystems may share a fundamental characteristic despite their differences, namely, organisational closure. Based on this kind of closure, scholars have also discussed health and malfunctional states in organisms. In this paper, we examine the possibility of expanding such an organisational approach to health and malfunctions to the ecological domain. Firstly, we will see that a malfunction is related to a lower effectiveness in the functional behaviour of some biotic components with respect to other systemic components. We will then show how some introduced species do not satisfactorily interact in an organisational closure with other ecosystem components, thus posing a threat to the self-maintenance of the ecosystem in which they are found. Accordingly, we will argue that an ecosystem can be said to be healthy when it is a vital environment organisationally grounded on its intrinsic capacity to ensure, under favourable conditions, appropriate functional behaviours for ecosystem components and ecosystem self-maintenance.

Cultural consensus and intracultural diversity in ethnotaxonomy: lessons from a fishing community in Northeast Brazil.

BACKGROUND: Traditional fishing communities are strongholds of ethnobiological knowledge but establishing to what degree they harbor cultural consensus about different aspects of this knowledge has been a challenge in many ethnobiological studies. METHODS: We conducted an ethnobiological study in an artisanal fishing community in northeast Brazil, where we interviewed 91 community members (49 men and 42 women) with different type of activities (fishers and non-fishers), in order to obtain free lists and salience indices of the fish they know. To establish whether there is cultural consensus in their traditional knowledge on fish, we engaged a smaller subset of 45 participants in triad tasks where they chose the most different fish out of 30 triads. We used the similarity matrices generated from the task results to detect if there is cultural consensus in the way fish were classified by them. RESULTS: The findings show how large is the community's knowledge of fish, with 197 ethnospecies registered, of which 33 species were detected as salient or important to the community. In general, men cited more fish than women. We also found that there was no cultural consensus in the ways fish were classified. CONCLUSIONS: Both free-listing and triad task methods revealed little cultural consensus in the way knowledge is structured and how fish were classified by community members. Our results suggest that it is prudent not to make assumptions that a given local community has a single cultural consensus model in classifying the organisms in their environment.

Beyond the divide between indigenous and academic knowledge: Causal and mechanistic explanations in a Brazilian fishing community.

Transdisciplinary research challenges the divide between Indigenous and academic knowledge by bringing together epistemic resources of heterogeneous stakeholders. The aim of this article is to explore causal explanations in a traditional fishing community in Brazil that provide resources for transdisciplinary collaboration, without neglecting differences between Indigenous and academic experts. Semi-structured interviews were carried out in a fishing village in the North shore of Bahia and our findings show that community members often rely on causal explanations for local ecological phenomena with different degrees of complexity. While these results demonstrate the ecological expertise of local community members, we also argue that recognition of local expertise needs to reflect on differences between epistemic communities by developing a culturally sensitive model of transdisciplinary knowledge negotiation.

A pragmatic approach for producing theoretical syntheses in ecology.

It has been proposed that ecological theory develops in a pragmatic way. This implies that ecologists are free to decide what, from the knowledge available to them, they will use to build models and learn about phenomena. Because in fields that develop pragmatically knowledge generation is based on the decisions of individuals and not on a set of predefined axioms, the best way to produce theoretical synthesis in such fields is to assess what individuals are using to support scientific studies. Here, we present an approach for producing theoretical syntheses based on the propositions most frequently used to learn about a defined phenomenon. The approach consists of (i) defining a phenomenon of interest; (ii) defining a collective of scientists studying the phenomenon; (iii) surveying the scientific studies about the phenomenon published by this collective; (iv) identifying the most referred publications used in these studies; (v) identifying how the studies use the most referred publications to give support to their studies and learn about the phenomena; (vi) and from this, identifying general propositions on how the phenomenon is approached, viewed and described by the collective. We implemented the approach in a case study on the phenomenon of ecological succession, defining the collective as the scientists currently studying succession. We identified three propositions that synthesize the views of the defined collective about succession. The theoretical synthesis revealed that there is no clear division between "classical'' and "contemporary'' succession models, and that neutral models are being used to explain successional patterns alongside models based on niche assumptions. By implementing the pragmatic approach in a case study, we show that it can be successfully used to produce syntheses based on the actual activity of the scientific community studying the phenomenon. The connection between the resulting synthesis and research activity can be traced back through the methodological steps of the approach. This result can be used to understand how knowledge is being used in a field of study and can guide better informed decisions for future studies.

The instability of field experiments: building an experimental research tradition on the rocky seashores (1950-1985).

In many experimental sciences, like particle physics or molecular biology, the proper place for establishing facts is the laboratory. In the sciences of population biology, however, the laboratory is often seen as a poor approximation of what occurs in nature. Results obtained in the field are usually more convincing. This raises special problems: it is much more difficult to obtain stable, repeatable results in the field, where environmental conditions vary out of the experimenter's control, than in the laboratory. We examine here how this problem affected an influential experimental research tradition in community ecology, the study of the ecology of the rocky seashores. In the 1960s, a handful of North-American ecologists, most notably Joseph Connell, Robert Paine and Paul Dayton, made the rocky seashores a model study system for experimenting in the field. Their experiments were deceptively simple: they removed species living on the seashore and described the resulting effects on the local ecology. These experiments exerted a deep influence on community ecology. They provided evidence for speculative developments concerning the theory of interspecific competition, the factors responsible for species richness and the ecology of food webs. They also stimulated novel conceptual developments. In particular, Paine developed the predation hypothesis, which states that the presence of predators can favour species richness, before introducing the keystone species concept, according to which some species exert disproportionate effects on ecological systems. More broadly, these experiments gave support to a methodological trend in favour of field experimentation. Only controlled perturbations in the field, it seemed, provided a reliable method to get insights into the structure of ecological communities. However, as experiments were continued in time and repeated in different sites, divergent results appeared. We analyse here how intertidal researchers coped with the variability of environmental conditions and tried to stabilize their results. In the process, they reconsidered not only their early conclusions, but also the exclusive status given to field experiments. Expanding on this case study, we discuss some significant differences between laboratory and field experiments.

Comparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method.

Complex networks have been successfully applied to the characterization and modeling of complex systems in several distinct areas of Biological Sciences. Nevertheless, their utilization in phylogenetic analysis still needs to be widely tested, using different molecular data sets and taxonomic groups, and, also, by comparing complex networks approach to current methods in phylogenetic analysis. In this work, we compare all the four main methods of phylogenetic analysis (distance, maximum parsimony, maximum likelihood, and Bayesian) with a complex networks method that has been used to provide a phylogenetic classification based on a large number of protein sequences as those related to the chitin metabolic pathway and ATP-synthase subunits. In order to perform a close comparison to these methods, we selected Basidiomycota fungi as the taxonomic group and used a high-quality, manually curated and characterized database of chitin synthase sequences. This enzymatic protein plays a key role in the synthesis of one of the exclusive features of the fungal cell wall: the presence of chitin. The communities (modules) detected by the complex network method corresponded exactly to the groups retrieved by the phylogenetic inference methods. Additionally, we propose a bootstrap method for the complex network approach. The statistical results we have obtained with this method were also close to those obtained using traditional bootstrap methods.

Young Adults' Belief in Genetic Determinism, and Knowledge and Attitudes towards Modern Genetics and Genomics: The PUGGS Questionnaire.

In this paper we present the development and validation a comprehensive questionnaire to assess college students' knowledge about modern genetics and genomics, their belief in genetic determinism, and their attitudes towards applications of modern genetics and genomic-based technologies. Written in everyday language with minimal jargon, the Public Understanding and Attitudes towards Genetics and Genomics (PUGGS) questionnaire is intended for use in research on science education and public understanding of science, as a means to investigate relationships between knowledge, determinism and attitudes about modern genetics, which are to date little understood. We developed a set of core ideas and initial items from reviewing the scientific literature on genetics and previous studies on public and student knowledge and attitudes about genetics. Seventeen international experts from different fields (e.g., genetics, education, philosophy of science) reviewed the initial items and their feedback was used to revise the questionnaire. We validated the questionnaire in two pilot tests with samples of university freshmen students. The final questionnaire contains 45 items, including both multiple choice and Likert scale response formats. Cronbach alpha showed good reliability for each section of the questionnaire. In conclusion, the PUGGS questionnaire is a reliable tool for investigating public understanding and attitudes towards modern genetics and genomic-based technologies.

What are the Evolutionary Origins of Mitochondria? A Complex Network Approach.

Mitochondria originated endosymbiotically from an Alphaproteobacteria-like ancestor. However, it is still uncertain which extant group of Alphaproteobacteria is phylogenetically closer to the mitochondrial ancestor. The proposed groups comprise the order Rickettsiales, the family Rhodospirillaceae, and the genus Rickettsia. In this study, we apply a new complex network approach to investigate the evolutionary origins of mitochondria, analyzing protein sequences modules in a critical network obtained through a critical similarity threshold between the studied sequences. The dataset included three ATP synthase subunits (4, 6, and 9) and its alphaproteobacterial homologs (b, a, and c). In all the subunits, the results gave no support to the hypothesis that Rickettsiales are closely related to the mitochondrial ancestor. Our findings support the hypothesis that mitochondria share a common ancestor with a clade containing all Alphaproteobacteria orders, except Rickettsiales.

Apoptosis and apoptotic mimicry in Leishmania: an evolutionary perspective.

Apoptotic death and apoptotic mimicry are defined respectively as a non-accidental death and as the mimicking of an apoptotic-cell phenotype, usually by phosphatidylserine (PS) exposure. In the case of the murine infection by Leishmania spp, apoptotic death has been described in promastigotes and apoptotic mimicry in amastigotes. In both situations they are important events of the experimental murine infection by this parasite. In the present review we discuss what features we need to consider if we want to establish if a behavior shown by Leishmania is altruistic or not: does the behavior increases the fitness of organisms other than the one showing it? Does this behavior have a cost for the actor? If we manage to show that a given behavior is costly for the actor and beneficial for the recipient of the action, we will be able to establish it as altruistic. From this perspective, we can argue that apoptotic-like death and apoptotic mimicry are both altruistic with the latter representing a weaker altruistic behavior than the former.

Detecting network communities: an application to phylogenetic analysis.

This paper proposes a new method to identify communities in generally weighted complex networks and apply it to phylogenetic analysis. In this case, weights correspond to the similarity indexes among protein sequences, which can be used for network construction so that the network structure can be analyzed to recover phylogenetically useful information from its properties. The analyses discussed here are mainly based on the modular character of protein similarity networks, explored through the Newman-Girvan algorithm, with the help of the neighborhood matrix . The most relevant networks are found when the network topology changes abruptly revealing distinct modules related to the sets of organisms to which the proteins belong. Sound biological information can be retrieved by the computational routines used in the network approach, without using biological assumptions other than those incorporated by BLAST. Usually, all the main bacterial phyla and, in some cases, also some bacterial classes corresponded totally (100%) or to a great extent (>70%) to the modules. We checked for internal consistency in the obtained results, and we scored close to 84% of matches for community pertinence when comparisons between the results were performed. To illustrate how to use the network-based method, we employed data for enzymes involved in the chitin metabolic pathway that are present in more than 100 organisms from an original data set containing 1,695 organisms, downloaded from GenBank on May 19, 2007. A preliminary comparison between the outcomes of the network-based method and the results of methods based on Bayesian, distance, likelihood, and parsimony criteria suggests that the former is as reliable as these commonly used methods. We conclude that the network-based method can be used as a powerful tool for retrieving modularity information from weighted networks, which is useful for phylogenetic analysis.

A síndrome de Down e sua patogênese: considerações sobre o determinismo genético / Down syndrome and its pathogenesis: considerations about genetic determinism

O trabalho apresenta uma análise de fatores causais da síndrome de Down e sua patogênese. Faz também uma revisão da história natural dessa síndrome e dos efeitos da trissomia da banda cromossômica 21q22, considerada crítica para o distúrbio. Embora esse desequilíbrio cromossômico esteja necessariamente presente na síndrome de Down, a relevância do determinismo genético é questionada a partir da observação da possibilidade de desenvolvimento do potencial cognitivo em sujeitos afetados pela síndrome, após a aplicação de programas de estimulação neuromotora e psicopedagógicos

A sindrome de Down e sua patogenese: consideracoes sobre o determinismo genetico

O trabalho apresenta uma analise de fatores causais da sindrome de Down e sua patogenese. Faz tambem uma revisao da historia natural dessa sindrome e dos efeitos da trissomia da banda cormossomica 21q22, considerada critica para o disturbio. Embora esse desequilibrio cromossomico esteja necessariamente presente na sindorme de Down, a relevancia do determinismo genetico e questionada a partir da observacao da possibilidade de desenvolvimento potencial cognitivo em sujeitos afetados pela sindrome, apos a aplicacao de programas de estimulacao neuromotora e psicopedagogicos.