Modeling Techniques for the High-Resolution Interpretation of Cryo-Electron Microscopy Reconstructions

Essential biological processes are governed by organized, dynamic interactions between multiple biomolecular systems. Complexes are thus formed to enable the biological function and get dissembled as the process is completed. Examples of such processes include the translation of the messenger RNA into protein by the ribosome, the folding of proteins by chaperonins or the entry of viruses in host cells. Understanding these fundamental processes by characterizing the molecular mechanisms that enable then, would allow the (better) design of therapies and drugs. Such molecular mechanisms may be revealed trough the structural elucidation of the biomolecular assemblies at the core of these processes. Various experimental techniques may be applied to investigate the molecular architecture of biomolecular assemblies. High-resolution techniques, such as X-ray crystallography, may solve the atomic structure of the system, but are typically constrained to biomolecules of reduced flexibility and dimensions. In particular, X-ray crystallography requires the sample to form a three dimensional (3D) crystal lattice which is technically di‑cult, if not impossible, to obtain, especially for large, dynamic systems. Often these techniques solve the structure of the different constituent components within the assembly, but encounter difficulties when investigating the entire system. On the other hand, imaging techniques, such as cryo-electron microscopy (cryo-EM), are able to depict large systems in near-native environment, without requiring the formation of crystals. The structures solved by cryo-EM cover a wide range of resolutions, from very low level of detail where only the overall shape of the system is visible, to high-resolution that approach, but not yet reach, atomic level of detail. In this dissertation, several modeling methods are introduced to either integrate cryo-EM datasets with structural data from X-ray crystallography, or to directly interpret the cryo-EM reconstruction. Such computational techniques were developed with the goal of creating an atomic model for the cryo-EM data. The low-resolution reconstructions lack the level of detail to permit a direct atomic interpretation, i.e. one cannot reliably locate the atoms or amino-acid residues within the structure obtained by cryo-EM. Thereby one needs to consider additional information, for example, structural data from other sources such as X-ray crystallography, in order to enable such a high-resolution interpretation. Modeling techniques are thus developed to integrate the structural data from the different biophysical sources, examples including the work described in the manuscript I and II of this dissertation. At intermediate and high-resolution, cryo-EM reconstructions depict consistent 3D folds such as tubular features which in general correspond to alpha-helices. Such features can be annotated and later on used to build the atomic model of the system, see manuscript III as alternative. Three manuscripts are presented as part of the PhD dissertation, each introducing a computational technique that facilitates the interpretation of cryo-EM reconstructions. The first manuscript is an application paper that describes a heuristics to generate the atomic model for the protein envelope of the Rift Valley fever virus. The second manuscript introduces the evolutionary tabu search strategies to enable the integration of multiple component atomic structures with the cryo-EM map of their assembly. Finally, the third manuscript develops further the latter technique and apply it to annotate consistent 3D patterns in intermediate-resolution cryo-EM reconstructions. The first manuscript, titled An assembly model for Rift Valley fever virus, was submitted for publication in the Journal of Molecular Biology. The cryo-EM structure of the Rift Valley fever virus was previously solved at 27Å-resolution by Dr. Freiberg and collaborators. Such reconstruction shows the overall shape of the virus envelope, yet the reduced level of detail prevents the direct atomic interpretation. High-resolution structures are not yet available for the entire virus nor for the two different component glycoproteins that form its envelope. However, homology models may be generated for these glycoproteins based on similar structures that are available at atomic resolutions. The manuscript presents the steps required to identify an atomic model of the entire virus envelope, based on the low-resolution cryo-EM map of the envelope and the homology models of the two glycoproteins. Starting with the results of the exhaustive search to place the two glycoproteins, the model is built iterative by running multiple multi-body refinements to hierarchically generate models for the different regions of the envelope. The generated atomic model is supported by prior knowledge regarding virus biology and contains valuable information about the molecular architecture of the system. It provides the basis for further investigations seeking to reveal different processes in which the virus is involved such as assembly or fusion. The second manuscript was recently published in the of Journal of Structural Biology (doi:10.1016/j.jsb.2009.12.028) under the title Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions. This manuscript introduces the evolutionary tabu search strategies applied to enable a multi-body registration. This technique is a hybrid approach that combines a genetic algorithm with a tabu search strategy to promote the proper exploration of the high-dimensional search space. Similar to the Rift Valley fever virus, it is common that the structure of a large multi-component assembly is available at low-resolution from cryo-EM, while high-resolution structures are solved for the different components but lack for the entire system. Evolutionary tabu search strategies enable the building of an atomic model for the entire system by considering simultaneously the different components. Such registration indirectly introduces spatial constrains as all components need to be placed within the assembly, enabling the proper docked in the low-resolution map of the entire assembly. Along with the method description, the manuscript covers the validation, presenting the benefit of the technique in both synthetic and experimental test cases. Such approach successfully docked multiple components up to resolutions of 40Å. The third manuscript is entitled Evolutionary Bidirectional Expansion for the Annotation of Alpha Helices in Electron Cryo-Microscopy Reconstructions and was submitted for publication in the Journal of Structural Biology. The modeling approach described in this manuscript applies the evolutionary tabu search strategies in combination with the bidirectional expansion to annotate secondary structure elements in intermediate resolution cryo-EM reconstructions. In particular, secondary structure elements such as alpha helices show consistent patterns in cryo-EM data, and are visible as rod-like patterns of high density. The evolutionary tabu search strategy is applied to identify the placement of the different alpha helices, while the bidirectional expansion characterizes their length and curvature. The manuscript presents the validation of the approach at resolutions ranging between 6 and 14Å, a level of detail where alpha helices are visible. Up to resolution of 12 Å, the method measures sensitivities between 70-100% as estimated in experimental test cases, i.e. 70-100% of the alpha-helices were correctly predicted in an automatic manner in the experimental data. The three manuscripts presented in this PhD dissertation cover different computation methods for the integration and interpretation of cryo-EM reconstructions. The methods were developed in the molecular modeling software Sculptor (http://sculptor.biomachina.org) and are available for the scientific community interested in the multi-resolution modeling of cryo-EM data. The work spans a wide range of resolution covering multi-body refinement and registration at low-resolution along with annotation of consistent patterns at high-resolution. Such methods are essential for the modeling of cryo-EM data, and may be applied in other fields where similar spatial problems are encountered, such as medical imaging.

Foraminifera and microfossil occurence in Late Jurassic sediments of the North and South Atlantic

Biostratigraphical, taxonomical, and palaeocological results were obtained from Oxfordian to Tithonian foraminifers of the Northern and Southern Atlantic Ocean boreholes of the DSDP Legs 1, 11, 36, 41, 44, 50, and 79. An oversight on the cored Jurassic sections of the DSDP Legs 79 and the corresponding foraminiferal descriptions are given. The reddish brown, clayey and carbonaceous Cat Gap Formation (Oxfordian to Tithonian) of the Northern Atlantic Ocean, rich in radiolarians, yields less or more uniform, in most cases allochthonous foraminiferal faunas of Central European shelf character. No Callovian and Upper Tithonian foraminiferaI zones can be established. The zone of Pseudomarssonella durnortieri covers the Oxfordian/Kimmeridgian, the zone of Neobulimina atlantica the Kimmeridgian/Lower Tithonian interval. Characteristic foraminiferal faunas are missing since the Upper Tithonian to Valanginian for reason of a widely distributed regression which caused hiatuses observed all over the Northern Atlantic Ocean and in parts of Europe. The Upper Jurassic cannot be subdivided into single stages by foraminiferal biostratigraphy alone. The fovaminiferal zones established by Moullad (1984) covering a Callovian-Tithonian interval may be of some local importance in the Tethyan realm: It has too long-ranging foraminiferal species to be used as index marker in the word-wide DSDP boreholes. Some taxonomical confusion is caused because in former publications some foraminiferal species have got different names both in the Jurassic and Cretaceous. The foraminiferal biostratigraphy of drilled sections from DSDP boreholes is restricted by the drilling technique and for palaeo-oceanographical, biological, and geological reasons. Foraminiferal faunas from the DSDP originally described as ,,bathyal, or ,,abyssal,, have to be derived from shallower water. This contrasts the palaeo-water depths of 3000-4000 m which result from sedimentological and palaeo-geographical investigations.

Martina Chapanay : figura legendaria de las Lagunas de Guanacache

A partir de la lectura del romance "La santa de las travesías" de Julio Fernández Peláez, se pretende analizar cómo distintos aspectos del personaje histórico Martina Chapanay evolucionan hacia lo legendario conviertiéndola de bandolera en protectora y benefactora de la zona de la Lagunas de Guanacache. La biografía novelada de Mabel Pagano, Martina la montonera del Zonda brinda importantes datos históricos que permiten seguir el itinerario de la protagonista para lograr la conversión. Este cambio puede analizarse en tres momentos complementarios entre sí: en el primero la protagonista aparece como profunda conocedora de la región cuyana, en el segundo se presenta a Martina como bandolera y jefa de un grupo de salteadores, y en el tercer momento el pueblo ve en ella la posesión de dones misteriosos que le confieren una autoridad sobrenatural. La historia y las tradiciones se mezclan en la memoria popular para crear este personaje de leyenda.

Multi-year high-frequency current and water quality in-situ observations at the Guadiana Estuary

High-frequency data collected continuously over a multiyear time frame are required for investigating the various agents that drive ecological and hydrodynamic processes in estuaries. Here, we present water quality and current in-situ observations from a fixed monitoring station operating from 2008 to 2014 in the lower Guadiana Estuary, southern Portugal (37°11.30' N, 7°24.67' W). The data were recorded by a multi-parametric probe providing hourly records (temperature, salinity, chlorophyll, dissolved oxygen, turbidity, and pH) at a water depth of ~1 m, and by a bottom-mounted acoustic Doppler current profiler measuring the pressure, near-bottom temperature, and flow velocity through the water column every 15 min. The time-series data, in particular the probe ones, present substantial gaps arising from equipment failure and maintenance, which are ineluctable with this type of observations in harsh environments. However, prolonged (months-long) periods of multi-parametric observations during contrasted external forcing conditions are available. The raw data are reported together with flags indicating the quality status of each record. River discharge data from two hydrographic stations located near the estuary head are also provided to support data analysis and interpretation.

(Supplemet S1) Silicon oxide and Potassium + Sodium oxide from the PACManus hydrothermal area

This study presents a systematic analysis and interpretation of autonomous underwater vehicle-based microbathymetry combined with remotely operated vehicle (ROV) video recordings, rock analyses and temperaturemeasurements within the PACManus hydrothermal area located on Pual Ridge in the Bismarck Sea of eastern Manus Basin. The data obtained during research cruise Magellan-06 and So-216 provides a framework for understanding the relationship between the volcanism, tectonismand hydrothermal activity. PACManus is a submarine felsic vocanically-hosted hydrothermal area that hosts multiple vent fields locatedwithin several hundredmeters of one another but with different fluid chemistries, vent temperatures and morphologies. The total area of hydrothermal activity is estimated to be 20,279m**2. Themicrobathymetrymaps combinedwith the ROV video observations allow for precise high-resolution mapping estimates of the areal extents of hydrothermal activity.We find the distribution of hydrothermal fields in the PACManus area is primarily controlled by volcanic features that include lava domes, thick andmassive blocky lava flows, breccias and feeder dykes. Spatial variation in the permeability of local volcanic facies appears to control the distribution of venting within a field.We define a three-stage chronological sequence for the volcanic evolution of the PACManus based on lava flow morphology, sediment cover and lava SiO2 concentration. In Stage-1, sparsely to moderately porphyritic dacite lavas (68-69.8 wt.% SiO2) erupted to form domes or cryptodomes. In Stage-2, aphyric lava with slightly lower SiO2 concentrations (67.2-67.9 wt.% SiO2) formed jumbled and pillowed lava flows. In the most recent phase Stage-3, massive blocky lavaswith 69 to 72.5wt.% SiO2were erupted throughmultiple vents constructing a volcanic ridge identified as the PACManus neovolcanic zone. The transition between these stages may be gradual and related to progressive heating of a silicic magma following a recharge event of hot, mantle-derived melts.

In-situ sediment temperature and pore water chloride concentration at pockmarks of the Nigerian continental margin

A joint research expedition between the French IFREMER and the German MARUM was conducted in 2011 using the R/V 'Pourquoi pas?' to study gas hydrate distributions in a pockmark field (1141-1199 m below sea surface) at the continental margin of Nigeria. The seafloor drill rig MeBo of MARUM was used to recover sediments as deep as 56.74 m below seafloor. The presence of gas hydrates in specific core sections was deduced from temperature anomalies recorded during continuous records of infrared thermal scanning and anomalies in pore water chloride concentrations. In situ sediment temperature measurements showed elevated geothermal gradients of up to 258 °C/km in the center of the so-called pockmark A which is up to 4.6 times higher than that in the background sediment (72 °C/km). The gas hydrate distribution and thermal regime in the pockmark are largely controlled by the intensity, periodicity and direction of fluid flow. The joint interaction between fluid flow, gas hydrate formation and dissolution, and the thermal regime governs pockmark formation and evolution on the Nigerian continental margin.

Si and SixGe1-x NWs studied by Raman spectroscopy

Group IV nanostructures have attracted a great deal of attention because of their potential applications in optoelectronics and nanodevices. Raman spectroscopy has been extensively used to characterize nanostructures since it provides non destructive information about their size, by the adequate modeling of the phonon confinement effect. The Raman spectrum is also sensitive to other factors, as stress and temperature, which can mix with the size effects borrowing the interpretation of the Raman spectrum. We present herein an analysis of the Raman spectra obtained for Si and SiGe nanowires; the influence of the excitation conditions and the heat dissipation media are discussed in order to optimize the experimental conditions for reliable spectra acquisition and interpretation.

Optimización de los procesos de medida e interpretación de la tomografía geoeléctrica en la prospección superficial

Debido al carácter innovador de los objetivos científico-tecnológicos planteados al inicio de la presente Tesis doctoral, además de la primera recopilación bibliográfica, a lo largo del desarrollo de la misma se ha realizado una actualización bibliográfica continua centrada en los desarrollos relativos a la instrumentación, las aplicaciones y los procesos de interpretación de las técnicas de tomografía eléctrica. Durante el desarrollo del presente trabajo, se han realizado una serie de campañas diferenciadas, tanto por los ambientes geológicos y las condiciones antrópicas en los que se han efectuado los perfiles geoeléctricos, como por la profundidad y los objetivos de la prospección. En esas campañas se han obtenido, mediante el programa Res2DInv, las secciones tomográficas con la configuración de variables por defecto y se ha realizado una interpretación estructural de las mismas. Como parte central del desarrollo de esta investigación se han efectuado varios procesos de optimización: Comparación y optimización de los dispositivos empleados para la medición de perfiles de resistividad de cara a la obtención de secciones tomográficas que presenten la mayor resolución en distintos ambientes geológicos. Selección de los rangos de representación (lineales y logarítmicos) y de la gradación cromática que, pudiendo adoptarse de forma generalizada, permita la mejor interpretación gráfica para usuarios no avanzados. Diseño de criterios para la selección del factor de amortiguamiento, como parámetro crítico en los procesos de inversión tomográfica de perfiles geoeléctricos de superficie, de forma que los modelos resultantes alcancen la mejor relación entre fiabilidad y error respecto a los valores medidos. Paralelamente a los procesos anteriores se ha definido un índice de calidad de la inversión, que es directamente normalizado y que permite evaluar el grado en el que pueden considerarse fiables tanto los valores de resistividad obtenidos como su distribución espacial. El índice desarrollado (IRI) está basado en la influencia que tiene la resistividad inicial del modelo de inversión en los valores de cada una de las celdas de la malla de inversión. Tras un exhaustivo análisis estadístico se ha verificado que, a diferencia de otros índices utilizados hasta la fecha, dicho índice no está afectado ni por la profundidad de investigación y la resolución de los dispositivos, ni por la distribución de resistividades que presente el subsuelo. ABSTRACT Due to the innovative character of the scientific and technological objectives proposed at the beginning of this thesis, in addition to preparatory bibliographic reference, a constant bibliographic update on developments related to instrumentation, applications and interpretation processes for electric tomography has been performed all through the development of the work. Several measuring campaigns were performed during the development of the thesis. These campaigns, in which the geoelectric profiles were measured, varied in several aspects, both in the geological and anthropic conditions, and also in the depth and objectives of the prospection. Tomographic sections were obtained and interpretated by making use of the Res2DInv software configured with the default variables. As part of the core development in this research, several optimization processes have been done: Comparison and optimization of the devices used in the measurement of resistivity profiles. This optimization allows increasing the resolution of tomographic sections in different geological conditions. Selection of the best visual representation for the tomographic sections. This involves the selection of the range of values and type of scale (linear vs. logarithmic) as well as the chromatic graduation. This selection allows improving the interpretation of tomographic sections for the non-expert eye. Devising of criteria for the selection of the damping factor, as the critical parameter in processes of tomographic inversion of superficial geoelectrical profiles. The use of these criteria allows selecting the best factors to obtain the best ratio between reliability and error (in relation to the mean values) for the resulting model. In addition to the aforementioned processes, and as part of the work within this thesis, it has been defined a normalized quality index for inversion. This index allows evaluating the degree of reliability of the obtained resistivity values and spatial distribution. The developed index, termed IRI in the thesis, is based on the influence shown by the initial resistivity of the inversion model on the values of each of the cells of the inversion mesh. After an exhaustive statistical analysis it was verified that the IRI index is neither affected by the investigation depth, nor the resolution of the devices, nor the resistivity’s distribution of the sub soil. This independency is a unique characteristic of the IRI index, not present in other indexes developed and used till date.

Estimation of functional connectivity from electromagnetic signals and the amount of empirical data required

An increasing number of neuroimaging studies are concerned with the identification of interactions or statistical dependencies between brain areas. Dependencies between the activities of different brain regions can be quantified with functional connectivity measures such as the cross-correlation coefficient. An important factor limiting the accuracy of such measures is the amount of empirical data available. For event-related protocols, the amount of data also affects the temporal resolution of the analysis. We use analytical expressions to calculate the amount of empirical data needed to establish whether a certain level of dependency is significant when the time series are autocorrelated, as is the case for biological signals. These analytical results are then contrasted with estimates from simulations based on real data recorded with magnetoencephalography during a resting-state paradigm and during the presentation of visual stimuli. Results indicate that, for broadband signals, 50–100 s of data is required to detect a true underlying cross-correlations coefficient of 0.05. This corresponds to a resolution of a few hundred milliseconds for typical event-related recordings. The required time window increases for narrow band signals as frequency decreases. For instance, approximately 3 times as much data is necessary for signals in the alpha band. Important implications can be derived for the design and interpretation of experiments to characterize weak interactions, which are potentially important for brain processing.

The dicode workbench: A flexible framework for the integration of information and web services

Aiming to address requirements concerning integration of services in the context of ?big data?, this paper presents an innovative approach that (i) ensures a flexible, adaptable and scalable information and computation infrastructure, and (ii) exploits the competences of stakeholders and information workers to meaningfully confront information management issues such as information characterization, classification and interpretation, thus incorporating the underlying collective intelligence. Our approach pays much attention to the issues of usability and ease-of-use, not requiring any particular programming expertise from the end users. We report on a series of technical issues concerning the desired flexibility of the proposed integration framework and we provide related recommendations to developers of such solutions. Evaluation results are also discussed.

La ciudad editada: de Las Vegas a Nueva York (1972-1978): Venturi / Scott Brown / Koolhaas

Si hubiese un denominador común entre todas las artes en lo que ha venido llamándose postmodernidad, éste tendría mucho que ver con el final del origen de la obra. Desde la literatura y la música hasta las artes plásticas y la arquitectura, la superación de la modernidad ha estado caracterizada por la sustitución del concepto de creación por el de intervención artística, o lo que es lo mismo, la interpretación de lo que ya existe. A principios del siglo XX los conceptos modernos de creación y origen implicaban tener que desaprender y olvidar todo lo anterior con el ánimo de partir desde cero; incluso en un sentido material Mies sugería la construcción literal de la materia y su movimiento de acuerdo a unas leyes. A partir de la segunda mitad de siglo los planteamientos historicistas empezaron a surgir como reacción ante la amnesia y la supuesta originalidad de los modernos. En este contexto surgen los libros Learning from Las Vegas, 1972 y Delirious New York, 1978, ambos deudores en muchos aspectos con el anterior libro de Venturi, Complexity and Contradiction in Architecture, 1966. Estos dos libros sobre ciudades, alejándose decididamente de las tendencias historicistas de la época, proponían utilizar el análisis crítico de la realidad existente como vehículo para la teoría y el proyecto de manera simultánea, convirtiéndose indirectamente en Manifiestos. Si en un primer momento Venturi, Rossi y otros planteaban acabar con los límites formales establecidos por la modernidad, así como por cualquiera de los cánones anteriores, tomando la totalidad de la obra construida como sistema de referencia, - al igual que hiciera Eliot en literatura, - los libros de Las Vegas y Nueva York sugerían directamente borrar los límites de la propia disciplina, llegando a poner en duda ¿Qué puede ser considerado arquitectura? Sin embargo, debido precisamente a la ausencia total de límites y a la inmensidad del sistema referencial planteado, “todo puede ser arquitectura”, como apuntaba Hans Hollein en 1968, los libros proponen al mismo tiempo definir el campo de actuación de cada cual de manera individual. Los escritos sobre Las Vegas y Nueva York suponen por un lado la eliminación de los limites disciplinares y por otro, la delimitación de ámbitos de trabajo concretos para sus autores: los propios de cada una de las ciudades interpretadas. La primera parte de la Tesis, Lecciones, se ocupa del necesario proceso de aprendizaje y experimentación previo a la acción crítica propiamente dicha. Los arquitectos contemporáneos necesitan acumular material, conocimiento, documentación, experiencias... antes de lanzarse a proponer mediante la crítica y la edición; y al contrario que ocurría con los modernos, cuanto más abundante sea ese bagaje previo más rica será la interpretación. Las ciudades de Roma, Londres y Berlín se entienden por tanto como experiencias capaces de proporcionar a Venturi, Scott Brown y Koolhaas respectivamente, sus “personales diccionarios”, unas interminables imaginerías con las que posteriormente se enfrentarían a los análisis de Las Vegas y Nueva York. La segunda parte, Críticas, se centra en la producción teórica en sí: los dos libros de ciudades analizados en estrecha relación con el Complexity and Contradiction. El razonamiento analógico característico de estos libros ha servido de guía metodológica para la investigación, estableciéndose relaciones, no entre los propios escritos directamente, sino a través de trabajos pertenecientes a otras disciplinas. En primer lugar se plantea un importante paralelismo entre los métodos de análisis desarrollados en estos libros y los utilizados por la crítica literaria, observando que si el new criticism y el nuevo periodismo sirvieron de guía en los escritos de Venturi y Scott Brown, la nouvelle critique y su propuesta de identificación poética fueron el claro referente de Koolhaas al abordar Nueva York. Por otro lado, la relevancia ganada por la actividad de comisariado artístico y la aparición de la figura del curator, como autoridad capaz de utilizar la obra de arte por encima de las intenciones de su propio autor, sirve, al igual que la figura del editor, como reflejo de la acción transformadora y de apropiación llevada a cabo tanto en Learning from Las Vegas, como en Delirious New York. Por último y a lo largo de toda la investigación las figuras de Bergson y Baudelaire han servido como apoyo teórico. A través de la utilización que de sus ideas hicieron Venturi y Koolhaas respectivamente, se ha tratado de mostrar la proximidad de ambos planteamientos desde un punto de vista ideológico. La Inclusión propuesta por Venturi y la ironía utilizada por Koolhaas, la contradicción y la paradoja, no son sino el reflejo de lógicas que en ambos casos reaccionan al mismo tiempo contra idealismo y materialismo, contra modernidad y antimodernidad, en un continuo intento de ser lo uno y lo otro simultáneamente. ABSTRACT If there was a common denominator among all the arts in what has been called postmodernism, it would have much to do with the end of the origin of the artwork. From literature and music to fine arts and architecture, overcoming modernity has been characterized by replacing the concept of artistic creation by the one of intervention, in other words, the interpretation of what already exists. In the early twentieth century modern concepts of creation and origin involved unlearning and forgetting everything before with the firm intention of starting from scratch. Even in a material sense Mies suggested the literal construction of matter and its motion according to laws. From the mid-century historicist approaches began to emerge in response to the amnesia and originality alleged by moderns. In this context appeared the books Learning from Las Vegas, 1972 and Delirious New York, 1978, both debtors in many respects to the previous book by Venturi, Complexity and Contradiction in Architecture, 1966. These two books on cities, which broke away decidedly with the historicist trends of the time, proposed using critical analysis of the existing reality as a vehicle for theory and projecting at the same time, indirectly becoming manifests. If at first Venturi, Rossi and others pose to erase the formal limits set by modernity, as well as any of the canons before, taking the entire work built as a reference system, - as did Eliot in literature - the books on Las Vegas and New York proposed directly erasing the boundaries of the discipline itself, coming to question what could be considered architecture? However, and precisely because of the absence of limits and the immensity of the established framework, - “everything could be architecture” as Hans Hollein pointed in 1968, - the books suggested at the same time the definition of a field of action for each one individually. The cities of Las Vegas and New York represented on the one hand the elimination of disciplinary limits and on the other, the delimitation of specific areas of work to its authors: Those on each of the cities interpreted. The first part of the thesis, Lessons, attend to the necessary process of learning and experimentation before the critical action itself. Contemporary architects need to accumulate material, knowledge, information, experiences... before proposing through criticism and editing; and unlike happened with moderns, the most abundant this prior baggage is, the richest will be the interpretation. Rome, London and Berlin are therefore understood as experiences capable of providing Venturi, Scott Brown and Koolhaas respectively, their “personal dictionaries”, interminable imageries with which they would later face the analysis of Las Vegas and New York. The second part, Critiques, focuses on the theoretical production itself: the two books on both cities analyzed closely with the Complexity and Contradiction. The analogical reasoning characteristic of these books has served as a methodological guide for the research, establishing relationships, not directly between the writings themselves, but through works belonging to other disciplines. First, an important parallel is set between the methods of analysis developed in these books and those used by literary criticism, noting that if the new criticism and new journalism guided Venturi and Scott Brown´s writings, the nouvelle critique and its poetic identification were clear references for Koolhaas when addressing New York. On the other hand, the relevance gained by curating and the understanding of the figure of the curator as an authority capable to use artworks above the intentions of their authors, like the one of the Editor, reflects the appropriation and processing actions carried out both in Learning from Las Vegas, and Delirious New York. Finally and over all the research Bergson and Baudelaire figures resonate continuously. Through the use of their ideas done by Venturi and Koolhaas respectively, the research has tried to show the proximity of both approaches from an ideological point of view. Inclusion, as posed by Venturi and irony, as used by Koolhaas, contradiction and paradox are reflections of the logic that in both cases allow them to react simultaneously against idealism and materialism, against modernism and anti-modernism.

El vidrio y sus máscaras : el sueño de la arquitectura de cristal

Según Heidegger, la esencia de la arquitectura, de la construcción, descansa en un no espacio: en la materia con que se construyen las fronteras que otorgan espacios, irradiando sobre ellos aquello que los caracteriza. Si hay alguna materia, de las utilizadas por la arquitectura a lo largo de su historia para construir fronteras, que haya mantenido una especial relación con la luz y la visión, dando un carácter inconfundible a los espacios aviados por ellas, esta es el vidrio; algunas de las etimologías de su nombre: zakû (ser claro), hyalos (diáfano) o vitrum (ver), así lo evidencian. Posiblemente, sea la pregnancia de este modo fascinante de relacionarse con la luz, la que ha hecho del vidrio, a lo largo del tiempo que lleva siendo usado en arquitectura, y aún antes, el material que ha provocado en el imaginario humano la ilusión de ser aquel en que, en último término, podrían llegar a sublimarse todos los demás, dando lugar con ello a lo que en la tesis hemos denominado el sueño de la arquitectura de cristal. Siendo la luz, siempre, energía, consideraremos en la tesis luz-energía, a aquella que ilumina y calienta; es una luz científica y mesurable. Cuando la luz se “hace visible”, desvelando un mensaje “contenido” en el vidrio, hablaremos de luz-información. Esta luz, no puede medirse científicamente. La luz-energía y la luz-información, se manifiestan al conjuro de la arquitectura de vidrio. Es la segunda la que ha conformado las fronteras de vidrio enmascarado, y la que se estudia con más detenimiento en la tesis. Los distintos modos de usar en arquitectura la infinita combinatoria de las propiedades de absortancia, reflectancia, transmitancia y translucencia del vidrio, ha condicionado al hombre en su manera de “ver” el mundo. Unas veces, “inmerso” en él, puesto que solo lo separa del mismo, una frontera transparente, y “deseadamente” invisible: ese modo de usar el vidrio, ha sido el sueño imposible de una parte importante de la arquitectura del siglo XX. Otras veces, para “aislarse” de él, el hombre ha manipulado la luz y el vidrio para construir mundos diferentes. Las fronteras de vidrio enmascarado de color, mosaicos, vidrieras, pantallas y lo que hemos llamado vidrios complejos (con un cometido similar al que Schiller atribuía al coro en la tragedia griega, aislar a esta del “mundo real”, para mantener su libertad poética), son las fronteras que han construido el sueño posible de la arquitectura de cristal. Ambas actitudes, en distintos momentos de la historia de la arquitectura, han sido dos formas de querer materializar un mismo sueño. La capacidad del vidrio para adaptarse a tantos modos de presentarse ante nosotros, y a poder ser interpretado de tantas formas diferentes, es la que ha servido para dar título a la tesis, pues hasta en su faceta más transparente, el vidrio, de una forma o de otra, se ha mostrado siempre como un material enmascarado en el más amplio sentido de la palabra: se enmascara, incluso cuando apela a la transparencia o se convierte en espejo, para hacernos caer en la ilusión de que no está presente. Cuando el hombre construyó fronteras de vidrio e incluso antes, cuando soñó que con él podría llegar a construirlas, condensó en ellas toda la mítica, la mística y la epistemología en torno a la luz y la visión, dando lugar a una serie de arquetipos arquitectónicos. En la iglesia bizantina, la luz sobre, o la luz desde, los mosaicos, construyó una frontera titilante; y en la catedral gótica, la luz a través de las vidrieras construyó una frontera radiante; en ambos casos con el fin de alcanzar anagógicamente lo Inteligible. En el siglo XIX, con el descubrimiento de la electricidad y su incorporación a la arquitectura, las fronteras se vuelven fulgurantes, aviando, en este caso, el espacio urbano. Poco antes, en este mismo siglo, el espíritu del gótico tiene un efímero resurgir del que se nutrirá, a comienzos del siglo XX, el expresionismo cristalino, en el que la luz anagógica se hace laica. El espacio urbano fulgurante prefigurado por este movimiento y presente en las ciudades desde principios del siglo XX, fue potenciado a mediados de ese siglo con la aparición de las pantallas, extendiéndose desde entonces, imparable, por todo el planeta. La reciente emergencia de los vidrios complejos, ha abierto la posibilidad de construir fronteras a la carta (de vidrios de propiedades múltiples, seleccionadas de forma voluntaria y variable en cada momento). En principio, se pensó que, el uso de estos vidrios como cerramiento, podría llegar a constituirse como la panacea de los problemas del material relacionados con la luz-energía, sin necesidad de recurrir a “prótesis”, y manteniendo por tanto la seductora tersura de la fachada; aunque parece que, por ahora, esa posibilidad es, cuando menos, lejana. Sin embargo, en el campo de las megapantallas urbanas (y ,en general, en el de las pantallas de información), ubicuas actualmente en nuestras vidas, los vidrios complejos ayudan a construir los espesos velos de ilusión, que según Lefebvre sirven para mantener el capitalismo, siendo el último estadio de un desarrollo tecnológico, impuesto por el principio de economía del hombre, que como un metrónomo inexorable, y a modo de contrapunto, ha acompañado siempre (de nuevo en palabras de Lefebvre), a la necesidad del gasto, del juego, de la lucha, del arte, de la fiesta. La tecnología y el arte forman parte de la cultura producida por la sociedad y como señala Lévi-Strauss, esa cultura imprime orden; por el contrario, la sociedad, entendida como el conjunto de relaciones que los hombres mantienen entre sí, produce desorden. Del equilibrio entre esos extremos, surge el progreso, incluido el de la arquitectura. Las fronteras de vidrio que analizamos en la tesis –que avían espacios para la espiritualidad, el fasto y el espectáculo o, desde otro punto de vista, para las distintas manifestaciones del poder: la iglesia, la monarquía, el estado o el mercado– también han surgido de esa concomitancia entre el desorden y el orden; y forma parte de ese desorden, la aventura que ha impulsado al genio individual de místicos, alquimistas, geómetras, abades, reyes, inventores, poetas y arquitectos, a explorar, como escribe Apollinaire, vastos y extraños territorios donde el misterio en flor, se ofrece a quien quiera cogerlo, hogueras nuevas de colores nunca vistos, mil fantasmas imponderables a los que dar cuerpo. ABSTRACT According to Heidegger, the essence of architecture, building, lies in a non-space: the material that creates the boundaries from which something begins its presencing, radiating onto them that which characterizes them. If there is any single material amongst all those used throughout the history of architecture to build boundaries which has maintained a special relationship with light and vision, which has bestowed a distinctive character on spaces avid for them, it is glass. This is evidenced in some of its etymologies: zakû (to be clear), hyalos (transparent), vitrum (see). The rich potential of this fascinating way of relating to light in the history of the architectural use of glass, and even before, is possibly what has triggered the illusion in human imagination of being something that can ultimately sublimate all others, giving rise to what in this thesis we call The Dream of Crystal Architecture. Given that light is always energy, in this thesis we consider energy-light to be that which illuminates and warms. This is scientific, measurable light. When light "becomes visible" and reveals a message “contained” in glass, we speak of information-light. This light cannot be measured scientifically. Energy-light and information-light are manifested under the spell of glass architecture. The latter is what has shaped the boundaries of coloured glass, which is studied in this thesis. Architecture's different ways of using the infinite combinations of the absorptance, reflectance, transmittance and translucency of glass has affected the way we humans "see" the world. Sometimes we are "immersed" in it, since only an invisible, transparent boundary separates us from it: this use of glass has characterized a considerable part of 20th century architecture. In other cases, in order to "isolate" us from it, we have manipulated light and glass to build different worlds: the boundaries of glass "masked" by colour, mosaics, stained glass, screens and what we have called complex glazing, which plays a similar role to what Schiller attributed to the chorus in Greek tragedy, isolating it from the "real world" in order to maintain its poetic license. These are the boundaries that have built the viable dream of crystal architecture. These two approaches have been different ways of making same dream come true at different times in the history of architecture. The ability of glass to adapt to so many forms of manifestation, and interpretation, is what has given rise to the title of the thesis. Even in its most transparent facet, glass has one way or another always been a masking material in the broadest sense of the word: it is masked even when it invites transparency or becomes a mirror, triggering the illusion that it is not present. When man began to build glass boundaries, and even before, when he dreamed that he could build them, he condensed in them all the mythology, mysticism and epistemology concerning light and vision, which gave rise to a series of architectural archetypes. In the Byzantine church, light on or from mosaics created tenuous boundaries. In Gothic cathedrals, the light through the stained glass windows constructed radiant boundaries. In both cases the aim was to achieve, in an anagogical way, the Intelligible. In the 19th, the discovery of electricity and its use in architecture led to the production of dazzling boundaries, in this case employed in urban spaces. Earlier in the same century, the Gothic spirit had a short-lived revival, which in the early 20th century drew from crystalline expressionism in which anagogic light became secular. The dazzling urban space prefigured by this movement, present in cities since the early 20th century, was intensified in the mid-century with the emergence of screens, and since then it has spread unstoppably across the world. The recent emergence of complex glasses has made it possible to build boundaries on demand in glass with multiple properties, chosen at will and at whim at any time. Initially it was thought that the use of this glass as a wall could eventually become the panacea for the material problems related to energy-light, without needing to resort to "prosthesis" and thereby maintain the seductive smoothness of the facade. For now, that possibility seems remote, to say the least. In the realm of urban megascreens and information screens in general, now ubiquitous in our lives, complex glasses help to build the thick veils of illusion which, according to Lefebvre, serve to maintain capitalism. Like an inexorable metronome, in counterpoint, this ultimate state of technological development imposed by man's principle of economy has in fact always accompanied (again in the words of Lefebvre), the need to spend, play, fight, art, and party. Technology and art are part of the culture produced by society. As Levi-Strauss says, this culture imposes order. On the contrary, society, understood as a set of relationships amongst people, produces disorder. Progress, including that of architecture, arises from the balance between these two extremes. The glass boundaries analyzed in this thesis, which propitiate spaces for spirituality, pomp and spectacle or, from a different perspective, for the various manifestations of power: the church, the monarchy, the state and the market, have also emerged from the concomitance of order and disorder. One aspect of this disorder is the adventure that has inspired the individual genius of mystics, alchemists, surveyors, abbots, kings, inventors, poets and architects to explore, as Apollinaire says, vast, strange domains where flowering mystery offers itself to whoever wishes to pluck it, new fires, colours you have never seen before, a thousand intangible phantasms still awaiting reality.

Affect and the Problem of Evil

A central aspect of the problem of evil or the argument from evil is the intensity or quantity of suffering. This quantity is conceived of as something objective and fixed. But because our experience is in part constituted and interpreted by our effectual orientation, there is no such objective quantum of suffering. But where there is no objective quantum of suffering, the argument from evil collapses. Here we begin by examining the connection between the philosophical and existential dimensions of the problem of and argument from evil as suffering. Next we consider the role of the affect in the constitution and interpretation of experience generally, together with implications for the argument from suffering. Third, we look at how a key affectual element of the argument from evil might undercut that argument. And finally, we consider a proposal to categorize suffering as a species of moral or spiritual failure, as affectually wrong.

Cristianismo Arreligioso: uma análise do desenvolvimento e recepção da teologia de Dietrich Bonhoeffer

Esta dissertação é o resultado da pesquisa sobre a teologia de Dietrich Bonhoeffer a partir de seus próprios escritos e da recepção e interpretação de seu pensamento por teólogos que se dedicaram ao estudo de sua reflexão teológica após sua morte, especialmente no que diz respeito à sua proposta de um cristianismo arreligioso. Dentre estes teólogos destacam-se Eberhard Bethge, autor de uma detalhada biografia de Bonhoeffer, além de Robinson e Hamilton, autores que participam do movimento que ficou conhecido como Teologia Radical . O objetivo da pesquisa é exatamente esclarecer o significado da proposta de um cristianismo arreligioso em Bonhoeffer, bem como analisar suas críticas à religião e as possibilidades encontradas em sua compreensão cristológica para uma vivência cristã autêntica num mundo que se tornou adulto. (AU)