Infinitely long branches and an informal test of common ancestry

Background: The evidence for universal common ancestry (UCA) is vast and persuasive. A phylogenetic test has been proposed for quantifying its odds against independently originated sequences based on the comparison between one versus several trees. This test was successfully applied to a well-supported homologous sequence alignment, which was however criticized on the basis of simulations showing that alignments without any phylogenetic structure could mislead its conclusions.Results: Here we present a simplified version of this same counterexample, which can be interpreted as a tree with arbitrarily long branches, and where the UCA test fails again. We also present another case whereby any sufficiently similar alignment will favour UCA irrespective of the true independent origins for the sequences. Finally, we present a class of frequentist tests that perform better than the purportedly formal UCA test.Conclusion: Despite claims to the contrary, we show that the counterexamples successfully detected a drawback of the original UCA test, of relying on sequence similarity. In light of our own simulations, we therefore conclude that the UCA test as originally proposed should not be trusted unless convergence has already been ruled out a priori.Reviewers: This article was reviewed by Professor Eugene Koonin, Dr. Yuri I. Wolf and Professor William Martin

Sampaio Bruno e Leonardo Coimbra: Olhares cruzados sobre o marxismo

info:eu-repo/semantics/publishedVersio

Stochastic model of transcription initiation of closely spaced promoters in escherichia coli

Dissertação para obtenção do Grau de Mestre em Engenharia BiomédicaThe regulatory mechanisms of transcription allow organisms to quickly adapt to changes in their environment and often act during transcription initiation. Here, a stochastic model of transcription initiation at the nucleotide level is proposed to study the dynamics of RNA production in closely spaced promoters and their regulatory mechanisms. We study how different arrangements (convergent e divergent), distance between transcription start sites (TSS), and various kinetic parameters affect the dynamics of RNA production. Further, we analyze how the kinetics of various steps in transcription initiation can be regulated by varying locations of repressor binding sites. From the results, we observe that the rate limiting steps have strong influence in the kinetics of RNA production. We find that interferences between RNA polymerases in divergent overlapped and convergent geometries causes the distribution of time intervals between the production of consecutive RNA molecules from each TSS to increase in mean and standard deviation, which leads to stronger fluctuations in the temporal levels of RNA molecules. We observe that small changes in the distance between TSSs can lead to abrupt transitions in the dynamics of RNA production, particularly when this change changes the geometry from overlapped to non-overlapped promoters. From the study of the correlation in the choices of directionality and on the time series of RNA productions we show that by tuning the distances and directions of the two TSS one can obtain both negative and positive correlations. We further show that distinct repression mechanisms of transcription initiation in steps such as the open and closed complex formation and promoter escape have different effects on the dynamics of RNA production. The study of these models will help the study of how genetic circuits have evolved and assist in designing artificial genetic circuits with desired dynamics

Image Processing and Simulation Toolboxes of Microscopy Images of Bacterial Cells

Recent advances in microscopy imaging technology have allowed the characterization of the dynamics of cellular processes at the single-cell and single-molecule level. Particularly in bacterial cell studies, and using the E. coli as a case study, these techniques have been used to detect and track internal cell structures such as the Nucleoid and the Cell Wall and fluorescently tagged molecular aggregates such as FtsZ proteins, Min system proteins, inclusion bodies and all the different types of RNA molecules. These studies have been performed with using multi-modal, multi-process, time-lapse microscopy, producing both morphological and functional images. To facilitate the finding of relationships between cellular processes, from small-scale, such as gene expression, to large-scale, such as cell division, an image processing toolbox was implemented with several automatic and/or manual features such as, cell segmentation and tracking, intra-modal and intra-modal image registration, as well as the detection, counting and characterization of several cellular components. Two segmentation algorithms of cellular component were implemented, the first one based on the Gaussian Distribution and the second based on Thresholding and morphological structuring functions. These algorithms were used to perform the segmentation of Nucleoids and to identify the different stages of FtsZ Ring formation (allied with the use of machine learning algorithms), which allowed to understand how the temperature influences the physical properties of the Nucleoid and correlated those properties with the exclusion of protein aggregates from the center of the cell. Another study used the segmentation algorithms to study how the temperature affects the formation of the FtsZ Ring. The validation of the developed image processing methods and techniques has been based on benchmark databases manually produced and curated by experts. When dealing with thousands of cells and hundreds of images, these manually generated datasets can become the biggest cost in a research project. To expedite these studies in terms of time and lower the cost of the manual labour, an image simulation was implemented to generate realistic artificial images. The proposed image simulation toolbox can generate biologically inspired objects that mimic the spatial and temporal organization of bacterial cells and their processes, such as cell growth and division and cell motility, and cell morphology (shape, size and cluster organization). The image simulation toolbox was shown to be useful in the validation of three cell tracking algorithms: Simple Nearest-Neighbour, Nearest-Neighbour with Morphology and DBSCAN cluster identification algorithm. It was shown that the Simple Nearest-Neighbour still performed with great reliability when simulating objects with small velocities, while the other algorithms performed better for higher velocities and when there were larger clusters present

Apresentação - Docência: entre processos de objetivação e subjetivação de sujeitos e conhecimentos

A questão da docência constitui-se como temática clássica nos estudos do campo educacional. Ela envolve dimensões políticas, éticas, epistemológicas e ontológicas que se movimentam em direções e sentidos que dependem da perspectiva armada para ver. Argumentamos neste texto que o sentido de docência no qual interessa-nos investir é produzido em meio a processos de objetivação e subjetivação de sujeitos e conhecimentos. A partir de uma postura epistêmica pós-fundacional (MARCHART, 2009; LACLAU, 2005, 2011) que radicaliza a crítica aos subjetivismos transcendentais e aos objetivismos deterministas na interpretação do Social, optamos por construir nossas argumentações a partir de eixos que, em nosso entender, consistem em aporias que permitem, simultaneamente, compreender, problematizar e participar do processo de significação da docência. Universal/particular, subjetividade/objetividade, teoria/prática, ensino/aprendizagem, ciência/pedagogia e escola/universidade foram os eixos selecionados para participar do referido processo

Concentração Bancária, Lucratividade e Risco Sistêmico: uma abordagem de Contágio Indireto

We investigate the impact of the banking system concentration on the perception of financial institutions interdependencies, as measured by the correlations of their return on assets. This correlation is observed by the market, and may provide an indicator of systemic risk potential, which we argue represents an indirect contagion channel. By changing this correlation, the degree of concentration may change the systemic risk exposure of the banking sector. Our findings suggest the existence of an indirect contagion channel in Brazil, and that a more concentrated financial system is associated with an increase in the potential of systemic risk among banks with similar characteristics of credit volume, leverage and ownership (state or private-owned). Our findings call attention to the implications of financial system consolidation to the contagion of idiosyncratic shocks. Banking consolidation may bring benefits by improving the diversification of the portfolios of banks, reducing their idiosyncratic risks, but may also increase the systemic risk, by increasing the probability of an idiosyncratic shock be interpreted as an aggregate shock.

Direito fundamental à liberdade de reunião e controle de constitucionalidade de leis penais e de sua interpretação e aplicação: contribuição para o direito de reunião como sub-ramo autônomo do direito administrativo

  Resumo: Este é um estudo de caso antecedido por uma explanação sistemática de seus pressupostos teóricos. O caso é fictício, mas fortemente inspirado em uma decisão de Câmara do Tribunal Constitucional Federal alemão. Nela, tratava-se de avaliar a constitucionalidade de uma medida policial e sua confirmação judicial no contexto de uma contramanifestação a uma reunião que ocorria em local público. Para a sua solução, desenvolveu-se um parecer jurídico-constitucional cujo objeto é a situação jurídica presente no caso, com vistas a avaliar as chances de êxito de uma eventual ação judicial contra as medidas estatais (policiais e decisão judicial), considerando a hipótese da violação do direito fundamental à liberdade de reunião a ser testada. No que se refere aos pressupostos teóricos do caso e à conjuntura política e jurídica brasileira, tem-se o seguinte. Como ocorre em qualquer Estado democrático, também no Brasil sob a égide da Constituição Federal (CF) o entorno político-ideológico do direito fundamental à liberdade de reunião é tão notório quanto contraproducente, pelo menos quando se pensa na imprescindibilidade de uma abordagem especificamente técnico-jurídica constitucional. Há um déficit na discussão pátria que o presente ensaio visa a sanar à luz do direito comparado alemão. Conjugar, assistematicamente, o princípio democrático com a liberdade de reunião e seu suposto caráter instrumental em relação àquele não faz jus aos desafios hermenêuticos implícitos no complexo teor do art. 5º, XVI CF em que se positivou o direito fundamental à liberdade de reunião. Partindo de uma análise sistemática do texto constitucional, o presente ensaio apresenta definições jurídico-dogmáticas, metodologicamente disciplinadas, e analisa o teor do dispositivo, classificando suas locuções entre condições subjetivas para o exercício da liberdade de reunião e previsão implícita de seus limites constitucionais que, por sua vez, podem ser, atendido certo ônus argumentativo, concretamente traçados pelo legislador ordinário. Assim, uma legislação ordinária regulamentadora não poderia ser, de plano, descartada como inconstitucional. Também a interpretação e a aplicação dessa eventual lei regulamentadora, assim como no caso da interpretação de quaisquer outros dispositivos normativos pertinentes ao direito administrativo e penal em geral, devem ser interpretadas e aplicadas à luz do direito fundamental à liberdade de reunião, de tal sorte a serem observados os vínculos específicos de todos os órgãos estatais pertinentes às três funções estatais clássicas. Palavras-chave: Autoaplicabilidade de direitos fundamentais. Regulamentação da liberdade de reunião. Limites constitucionais da liberdade de reunião. Interpretação judicial à luz da liberdade de reunião.   Abstract: This is a case study preceded by a systematic explanation of its theoretical framework. The case is fictitious but strongly inspired by a judgement of the Federal Constitutional Court in Germany, in which the court assessed the constitutionality of a police measure and its judicial confirmation in the context of a counter-protest to a meeting that had occurred in a public space. For the case study’s resolution, it was developed a juridical-constitutional opinion centred on the juridical situation exposed on the case, with the aim to evaluate the chances of a positive outcome of an eventual judicial action against the state measures (police measure and its juridical confirmation), considering the hypothesis of violation of the fundamental right to assembly. As in any other democracy, in Brazil under the Federal Constitution (FC) of 1988, the political-ideological contours of the right to freedom of assembly are as notorious as they are counterproductive - at least when one thinks of the indispensability of a specific constitutional legal technique. There is a deficit in the Brazilian literature that the present essay seeks to remedy in the light of comparative law considering the German case. To reconcile the democratic principle with the freedom of assembly, without a systematic approach, one assumes its instrumental character in relation to the former and does not meet the hermeneutical challenges implicit in the complex content of article 5, XVI, of the Brazilian Federal Constitution, in which freedom of assembly was enshrined. From a systematic analysis of the constitutional text, this study presents legal-dogmatic definitions that are methodologically disciplined, and analyzes the content of the aforementioned constitutional article, classifying its parts as either subjective conditions for the exercise of freedom of assembly or as implicit constitutional limits, which can be concretely drawn by the ordinary legislator, provided that they observe certain argumentative burdens. Thus, such a regulatory legislation could not, prima facie, be considered unconstitutional. Also, its eventual interpretation and application -as the interpretation of any other normative provision of administrative or criminal law in general - must be done in the light of freedom of assembly in such a way that the specific bounds between all three state functions are respected. Keywords: Self-enforceability of fundamental rights. Regulation of the freedom of assembly. Constitutional limits of the freedom of assembly. Judicial interpretation in the light of the freedom of assembly

Alturas Inacessíveis: Uma Análise Histórica em Livros Didáticos de Matemática

Mesmo com todo o avanço tecnológico e todas as diversas fontes de informações disponibilizadas, o livro didático permanece como um importante recurso em sala de aula, de fácil acesso para alunos e professores, sendo, assim, o mais usual. Isso tem gerando um aumento significativo nas pesquisas sobre livros didáticos, cada uma com sua peculiaridade. Nessa linha, e para contribuir com essa análise, esta pesquisa pretende responder ao seguinte questionamento: Como os livros didáticos de matemática têm abordado, ao longo da história, as deduções da altura de objetos, cuja base é inacessível? Tem como objetivo geral discutir, historicamente, as deduções da altura de objetos com bases inacessíveis, presentes nos livros didáticos de Matemática e, nos objetivos específicos, apresentar o histórico do livro didático no Brasil; discorrer sobre a trigonometria no triângulo retângulo; ilustrar a proposta da pesquisa; apresentar as deduções propostas para o ensino da trigonometria; e analisar as explicações, exemplos, atividades de livros didáticos desde 1929. Como alicerce teórico, a pesquisa primou em apresentar a evolução histórica dos livros didáticos e, em seguida, discutir o ensino da trigonometria no Brasil. A pesquisa é de caráter documental, realizou análises em livros didáticos e buscou, insistentemente, alcançar os objetivos propostos por meio das análises feitas nas explicações, deduções, exemplos, exercícios e, inclusive, figuras. As análises evidenciaram que nem sempre o conteúdo variações entre ângulos notáveis eram abordados nos livros didáticos. Há uma defasagem de duas décadas, até o início da década de 50, quando, finalmente, essa parte da trigonometria começou a constar nesses livros. As análises apontam que os autores utilizam três métodos em suas obras: a lei geral, o sistema de equações e as propriedades do triângulo. A pesquisa propõe possíveis deduções para determinar a altura de objetos cuja distância até a base é inacessível, por meio da variação de ângulos notáveis. Tais propostas tornam-se um material importante para os professores de Matemática, que poderão utilizá-las para estimular no aluno a aprendizagem desse conteúdo, bem como aproximá-lo de outras situações e/ou padrões matemáticos com esse conteúdo e, assim, aumentar seu rendimento do aluno, entre outros.Even with all the technological advancement and all the sources of information available, the textbook will become an important resource in the classroom, easily accessible for classes and teachers, and thus the most usual. This has a greater weight in searches on textbooks, each with its peculiarity. In this line, and to contribute to this analysis, this research intends to answer the following question: How did the textbooks of mathematics have approached, throughout history, the deductions of the height of objects, whose base is inaccessible? It has as general objective to discuss, historically, the deductions of the height of objects with inaccessible bases, present in the textbooks of Mathematics and, in the specific objectives, to present the history of the textbook in Brazil; talk about trigonometry in the triangle rectangle; illustrate the research proposal; present the proposed deductions for the teaching of trigonometry; and analyze the explanations, examples, textbook activities since 1929. As a theoretical foundation, the research focused on presenting the historical evolution of textbooks and then discussing the teaching of trigonometry in Brazil. The research is documentary in nature, carried out analysis in didactic books and sought, persistently, to reach the proposed objectives through the analyzes made in the explanations, deductions, examples, exercises and even figures. The analyzes showed that not always the content variations between notable angles were addressed in textbooks. There is a delay of two decades, until the early 1950s, when, finally, this part of trigonometry began to appear in these books. The analyzes indicate that the authors use three methods in their works: the general law, the system of equations and the properties of the triangle. The research proposes possible deductions to determine the height of objects whose distance to the base is inaccessible, through the variation of notable angles. Such proposals become important material for teachers of Mathematics, who can use them to stimulate in the student the learning of this content, as well as to bring it closer to other mathematical situations and/or patterns with this content and, thus, to increase its student achievement, among others

Questões Constitucionais na Ordem Processual: entre a Repercussão Geral e a Tutela de Direitos Fundamentais Individuais

Art. 102, §3° of the Brazilian Federal Constitution was enacted by a constitutional amendment in 2004 and established an qualitative filter to be applied by the Supreme Court in a kind of extraordinary judgment concerning the admissibility of Extraordinary Appeals. The purpose is to enable the Court to justify the dismissal of Extraordinary Appeals whose “constitutional issues” do not have “general repercussion” in a move to secure that Court's functional capacity. As such, the aforementioned filter generally applies to cases that do not have social, political, economic or even legal relevance. There is not yet a definition or adequately classification of that concepts. . On the one hand, the specialized discussion has focused on the concept of “general repercussions” whose meaning, nevertheless, has been only unsatisfactorily clarified. On the other hand, there is no study to systematize the role of the concept of “constitutional questions”, which is a presupposition to the provision of “general repercussion”. The present study aims to fill this gap.  The bibliographical sources used span vast comparative literature regarding a related problem in Germany as well as the criticism concerning the legal-scientific investigation of the delimitation between the so-called “specific” constitutional law and infra-constitutional law. The study confirms the hypothesis that, although the content of art. 102, §3° of the Brazilian Constitution, it would be the duty of the competent judge to recognize these issues ex officio. As a result, the study presents criteria of orientation on the conceptual and practical delineation of the “constitutional questions”.O art. 102, §3° CF, inserido pelo constituinte derivado em 2004, instituiu filtro aparentemente qualitativo a ser aplicado pelo STF em sede de juízo extraordinário de admissibilidade de Recursos Extraordinários. O propósito é, em suma, viabilizar a fundamentação pela Corte do descarte de Recursos Extraordinários, cujas “questões constitucionais” não tenham “repercussão geral”, com vistas à garantia de sua capacidade funcional ameaçada por uma sobrecarga de recursos a serem julgados. Como tais entendidos, são os recursos que não tenham relevância social, política, econômica ou até jurídica. Passados 14 anos desde sua inserção no texto constitucional não se logrou definir e adequadamente classificar o novo instituto processual-constitucional com fortes implicações jurídico-materiais. A discussão enfoca o conceito de “repercussões gerais” que foi ainda apenas insatisfatoriamente, mas de certo modo concretizado. Por sua vez, sobre o conceito de “questões constitucionais”, que representa o pressuposto daquele, não existe nenhum estudo específico. O presente estudo visa a suprir essa lacuna. Como método, valeu-se do chamado princípio distributivo cunhado no direito germânico. Em seu inventário de fontes, consta um vasto material comparativo relativo especialmente à lida jurisprudencial com o problema correlato na Alemanha, além da crítica à delimitação entre o chamado direito constitucional “específico” e o direito infraconstitucional. Partindo da hipótese segundo a qual, a despeito do teor do art. 102, 3° CF, seria dever do juiz natural das questões constitucionais reconhecê-las ex officio, o estudo conclui por sua confirmação. Como resultado, apresenta critérios de orientação para o delineamento conceitual e prático das “questões constitucionais”