Species occurrence records from online databases are an indispensable resource in ecological, biogeographical and palaeontological research. However, issues with data quality, especially incorrect ...geo‐referencing or dating, can diminish their usefulness. Manual cleaning is time‐consuming, error prone, difficult to reproduce and limited to known geographical areas and taxonomic groups, making it impractical for datasets with thousands or millions of records.
Here, we present CoordinateCleaner, an r‐package to scan datasets of species occurrence records for geo‐referencing and dating imprecisions and data entry errors in a standardized and reproducible way. CoordinateCleaner is tailored to problems common in biological and palaeontological databases and can handle datasets with millions of records. The software includes (a) functions to flag potentially problematic coordinate records based on geographical gazetteers, (b) a global database of 9,691 geo‐referenced biodiversity institutions to identify records that are likely from horticulture or captivity, (c) novel algorithms to identify datasets with rasterized data, conversion errors and strong decimal rounding and (d) spatio‐temporal tests for fossils.
We describe the individual functions available in CoordinateCleaner and demonstrate them on more than 90 million occurrences of flowering plants from the Global Biodiversity Information Facility (GBIF) and 19,000 fossil occurrences from the Palaeobiology Database (PBDB). We find that in GBIF more than 3.4 million records (3.7%) are potentially problematic and that 179 of the tested contributing datasets (18.5%) might be biased by rasterized coordinates. In PBDB, 1205 records (6.3%) are potentially problematic.
All cleaning functions and the biodiversity institution database are open‐source and available within the CoordinateCleaner r‐package.
Comprehending complex systems by simplifying and highlighting important dynamical patterns requires modeling and mapping higher-order network flows. However, complex systems come in many forms and ...demand a range of representations, including memory and multilayer networks, which in turn call for versatile community-detection algorithms to reveal important modular regularities in the flows. Here we show that various forms of higher-order network flows can be represented in a unified way with networks that distinguish physical nodes for representing a complex system’s objects from state nodes for describing flows between the objects. Moreover, these so-called sparse memory networks allow the information-theoretic community detection method known as the map equation to identify overlapping and nested flow modules in data from a range of different higher-order interactions such as multistep, multi-source, and temporal data. We derive the map equation applied to sparse memory networks and describe its search algorithm Infomap, which can exploit the flexibility of sparse memory networks. Together they provide a general solution to reveal overlapping modular patterns in higher-order flows through complex systems.
ABSTRACTCurrent research on post-truth politics often portrays a war waged by anti-science populists against pure, truth-seeking scientists. This critical framework was replicated in Brazil, where ...the former President Jair Bolsonaro was accused of neglecting scientific expertise to promote alternative treatments for the COVID-19 pandemic. Bolsonaro was deemed responsible for replacing sound scientific evidence with religious and ideological claims, resulting in many deaths. In this article, we investigate public controversies surrounding chloroquine (HCQ) and indicate that Bolsonaro’s discourses were not based on anti-science statements, as the literature on post-truth politics often emphasizes. Instead, Bolsonaro invoked the symbols of modern science and claimed to have the actual experts on his side. Thus, we argue that to understand the challenge posed by far-right populists to scientific institutions, we need to employ analytical instruments that help us complicate easy demarcations of facts and stark binaries of science/anti-science.
Abstract
Hypergraphs offer an explicit formalism to describe multibody interactions in complex systems. To connect dynamics and function in systems with these higher-order interactions, network ...scientists have generalised random-walk models to hypergraphs and studied the multibody effects on flow-based centrality measures. Mapping the large-scale structure of those flows requires effective community detection methods applied to cogent network representations. For different hypergraph data and research questions, which combination of random-walk model and network representation is best? We define unipartite, bipartite, and multilayer network representations of hypergraph flows and explore how they and the underlying random-walk model change the number, size, depth, and overlap of identified multilevel communities. These results help researchers choose the appropriate modelling approach when mapping flows on hypergraphs.
Resumo Políticas de controle da pandemia de Covid-19 têm sido alvo de disputas no Brasil, com autoridades divergindo sobre formas de tratamento e os efeitos das estratégias de distanciamento social. ...Análises recentes caracterizam tais disputas como uma “batalha ideológica” de Bolsonaro contra “argumentos racionais” de especialistas e da OMS. Além disso, críticos caracterizam Bolsonaro como um representante do “populismo científico” que produz fake news para sustentar pautas negacionistas. Neste artigo, dialogamos com o campo de estudos de Ciência, Tecnologia e Sociedade (CTS) para analisar os usos da ciência durante a pandemia. Demostramos que Bolsonaro não nega enunciados científicos in toto, mas busca legitimar suas políticas de saúde a partir das controvérsias públicas sobre a ciência. Ao explorar os meandros da produção de fatos científicos, o que Bolsonaro faz é questionar as credenciais da OMS e acusar opositores de politizarem pesquisas sobre formas de contenção da pandemia. Em outras palavras, Bolsonaro e seu entorno avançam uma imagem transcendental da Ciência, que reifica a divisão moderna entre o saber científico e a cultura, para criticar a contaminação ideológica de algumas instituições científicas no período de pandemia. Tal postura revela o jogo de poder epistêmico intrínseco ao debate contemporâneo sobre pós-verdade, no qual ideologia, esoterismo e desrazão são atribuídos sempre ao enunciado do outro.
Abstract The politics of Covid-19’s pandemic control in Brazil has been engulfed in disputes, with local authorities disagreeing about alternatives of health treatment and the effects of social distancing strategies. Recent analyses have characterized such disputes as Bolsonaro’s “ideological battle” against “rational arguments” of specialists and the WHO. Also, critics have described Bolsonaro as a representative of “scientific populism” who produces fake news to support his anti-science politics. In this article, we engage with the field of Science and Technology Studies (STS) to observe the multiple uses of science during the pandemic. We argue that Bolsonaro does not deny scientific statements in toto but seeks to legitimize his government’s health politics based upon public controversies about science. Bolsonaro explores the interstices of the making of scientific facts to question WHO’s credibility and to accuse his adversaries of politicizing scientific research during the pandemic. Thus, Bolsonaro sustains a transcendental image of science, which reifies the modern separation between science knowledge and culture, to criticize the ideological contamination of certain institutions. This posture reveals the epistemic dispute intrinsic to contemporary debates on post-truth, which postulates that ideology, esoterism, and anti-reason are always attributes of others.
We are witnessing an upsurge in crime forecasting software, which supposedly draws predictive knowledge from data on past crime. Although prevention and anticipation are already embedded in the ...apparatuses of government, going beyond a mere abstract aspiration, the latest innovations hold out the promise of replacing police officers’ “gut feelings” and discretionary risk assessments with algorithmic-powered, quantified analyses of risk scores. While police departments and private companies praise such innovations for their cost-effective rationale, critics raise concerns regarding their potential for discriminating against poor, black, and migrant communities. In this article, I address such controversies by telling the story of the making of CrimeRadar, an app developed by a Rio de Janeiro-based think tank in partnership with private associates and local police authorities. Drawing mostly on Latour’s contributions to the emerging literature on security assemblages, I argue that we gain explanatory and critical leverage by looking into the mundane practices of making and unmaking sociotechnical arrangements. That is, I address the chain of translations through which crime data are collected, organized, and transformed into risk scores. In every step, new ways of seeing and presenting crime are produced, with a significant impact on how we experience and act upon (in)security.
New network models of complex systems use layers, state nodes, or hyperedges to capture higher-order interactions and dynamics. Simplifying how the higher-order networks change over time or depending ...on the network model would be easy with alluvial diagrams, which visualize community splits and merges between networks. However, alluvial diagrams were developed for networks with regular nodes assigned to non-overlapping flat communities. How should they be defined for nodes in layers, state nodes, or hyperedges? How can they depict multilevel, overlapping communities? Here we generalize alluvial diagrams to map change in higher-order networks and provide an interactive tool for anyone to generate alluvial diagrams. We use the alluvial diagram generator in three case studies to illustrate significant changes in the organization of science, the effect of modeling network flows with memory in a citation network and distinguishing multidisciplinary from field-specific journals, and the effects of multilayer representation of a collaboration hypergraph.
Abstract The COVID-19 pandemic has sparked controversies over health security strategies adopted in different countries. The urge to curb the spread of the virus has supported policies to restrict ...mobility and to build up state surveillance, which might induce authoritarian forms of government. In this context, the Copenhagen School has offered an analytical repertoire that informs many analyses in the fields of critical security studies and global health. Accordingly, the securitisation of COVID-19 might be necessary to deal with the crisis, but it risks unfolding discriminatory practices and undemocratic regimes, with potentially enduring effects. In this article, we look into controversies over pandemic-control strategies to discuss the political and analytical limitations of securitisation theory. On the one hand, we demonstrate that the focus on moments of rupture and exception conceals security practices that unfold in ongoing institutional disputes and over the construction of legitimate knowledge about public health. On the other hand, we point out that securitisation theory hinders a genealogy of modern apparatuses of control and neglects violent forms of government which are manifested not in major disruptive acts, but in the everyday dynamics of unequal societies. We conclude by suggesting that an analysis of the bureaucratic disputes and scientific controversies that constitute health security knowledges and practices enables critical approaches to engage with the multiple – and, at times, mundane – processes in which (in)security is produced, circulated, and contested.
Resumo A pandemia de COVID-19 tem gerado controvérsias em torno das políticas de saúde adotadas em diferentes países. A necessidade de controlar a propagação do vírus tem sido usada como justificativa para medidas de restrição da mobilidade e para largos investimentos em dispositivos de vigilância, o que pode abrir espaço para formas não democráticas de governo. Nesse contexto, a Escola de Copenhague tem oferecido o instrumental teórico que informa muitas das análises nos campos de estudos críticos de segurança e saúde global. Segundo esta perspectiva, a securitização da COVID-19 agiliza as respostas à crise, mas guarda caráter discriminatório, contribuindo ainda para o avanço de políticas autoritárias potencialmente duradouras. Neste artigo, exploramos os debates recentes em torno das políticas de contenção da pandemia para abordar os limites políticos e analíticos da teoria da securitização. Por um lado, demonstramos que o foco em momentos de ruptura e políticas de exceção negligencia práticas de segurança que se desenvolvem no dia a dia das disputas institucionais e na construção de conhecimento especializado sobre saúde pública. Por outro, apontamos que a proposta da Escola de Copenhague impede uma genealogia dos aparatos modernos de segurança e ignora formas violentas de governo que não se manifestam em grandes atos disruptivos, mas na rotina de sociedades desiguais. Sugerimos, por fim, que a análise das disputas burocráticas e controvérsias científicas que constituem os conhecimentos e práticas dos campos de segurança e saúde permite que abordagens críticas se engajem com os múltiplos e, por vezes, mundanos processos pelos quais a (in)segurança é produzida, disseminada e contestada.
raxmlGUI is a graphical user interface to RAxML, one of the most popular and widely used softwares for phylogenetic inference using maximum likelihood.
Here we present raxmlGUI 2.0, a complete ...rewrite of the GUI which seamlessly integrates RAxML binaries for all major operating systems with an intuitive graphical front‐end to setup and run phylogenetic analyses.
Our program offers automated pipelines for analyses that require multiple successive calls of RAxML, built‐in functions to concatenate alignment files while automatically specifying the appropriate partition settings, and one‐click model testing to select the best substitution models using ModelTest‐NG. In addition to RAxML 8.x, raxmlGUI 2.0 also supports the new RAxML‐NG, which provides new functionality and higher performance on large datasets.
raxmlGUI 2.0 facilitates phylogenetic analyses by coupling an intuitive interface with the unmatched performance of RAxML.
Buoyancy is a well-known effect in immiscible binary Bose-Einstein condensates. Depending on the differential confinement experienced by the two components, a bubble of one component sitting at the ...center of the other eventually floats to the surface, around which it spreads either totally or partially. We discuss how quantum fluctuations may significantly change the volume and position of immiscible bubbles. We consider the particular case of two miscible components, forming a pseudoscalar bubble condensate with enhanced quantum fluctuations (quantum bubble), immersed in a bath provided by a third component, with which they are immiscible. We show that in such a peculiar effective binary mixture, quantum fluctuations change the equilibrium of pressures that define the bubble volume and modify as well the criterion for buoyancy. Once buoyancy sets in, in contrast to the mean-field case, quantum fluctuations may place the bubble at an intermediate position between the center and the surface. At the surface, the quantum bubble may transition into a floating self-bound droplet.
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