Evolution of genetic organization in digital organisms

We examine the evolution of expression patterns and the organization of genetic information in populations of self-replicating digital organisms. Seeding the experiments with a linearly expressed ancestor, we witness the development of complex, parallel secondary expression patterns. Using principles from information theory, we demonstrate an evolutionary pressure towards overlapping expressions causing variation (and hence further evolution) to sharply drop. Finally, we compare the overlapping sections of dominant genomes to those portions which are singly expressed and observe a significant difference in the entropy of their encoding.Comment: 18 pages with 5 embedded figures. Proc. of DIMACS workshop on "Evolution as Computation", Jan. 11-12, Princeton, NJ. L. Landweber and E. Winfree, eds. (Springer, 1999

Fossil clitellate annelid cocoons and their microbiological inclusions from the Eocene of Seymour Island, Antarctica

Clitellate annelids have a meagre body fossil record but they secrete proteinaceous cocoons for the protection of eggs that, after hardening, are readily fossilized and offer a largely untapped resource for assessing the evolutionary history of this group. We describe three species of clitellate cocoons (viz., Burejospermum seymourense sp. nov., B. punctatum sp. nov. and Pegmatothylakos manumii gen. et sp. nov.) from the lower Eocene La Meseta Formation, Seymour Island, Antarctica. The cocoons probably derive from continental settings and were transported to, and preserved within, nearshore marine to estuarine environments. The cocoons provide the first evidence of commensal or parasitic relationships in the Eocene continental ecosystemsof Antarctica. Moreover, numerous micro-organisms and the oldest fossilizedexamples of animal spermatozoa are preserved as moulds within the consolidatedwalls of the cocoons. Fossil annelid cocoons offer potential for enhanced palaeoenvironmental interpretation of sediments, correlation between continental and shallowmarine strata, and improved understanding of the development of clitellate annelid reproductive traits and the evolutionary history of soft-bodied micro-organisms in general.Facultad de Ciencias Naturales y Muse

Hierarchical object-based mapping of riverscape units and in-stream mesohabitats using LiDAR and VHR imagery

In this paper, we present a new, semi-automated methodology for mapping hydromorphological indicators of rivers at a regional scale using multisource remote sensing (RS) data. This novel approach is based on the integration of spectral and topographic information within a multilevel, geographic, object-based image analysis (GEOBIA). Different segmentation levels were generated based on the two sources of RS data, namely very-high spatial resolution, near-infrared imagery (VHR) and high-resolution LiDAR topography. At each level, different input object features were tested with Machine Learning classifiers for mapping riverscape units and in-stream mesohabitats. The GEOBIA approach proved to be a powerful tool for analyzing the river system at different levels of detail and for coupling spectral and topographic datasets, allowing for the delineation of the natural fluvial corridor with its primary riverscape units (e.g., water channel, unvegetated sediment bars, riparian densely-vegetated units, etc..) and in-stream mesohabitats with a high level of accuracy, respectively of K=0.91 and K=0.83. This method is flexible and can be adapted to different sources of data, with the potential to be implemented at regional scales in the future. The analyzed dataset, composed of VHR imagery and LiDAR data, is nowadays increasingly available at larger scales, notably through European Member States. At the same time, this methodology provides a tool for monitoring and characterizing the hydromorphological status of river systems continuously along the entire channel network and coherently through time, opening novel and significant perspectives to the river science and management, notably for planning and targeting actions.JRC.H.1-Water Resource

Natural Selection, Adaptive Evolution and Diversity in Computational Ecosystems

The central goal of this thesis is to provide additional criteria towards implementing open-ended evolution in an artificial system. Methods inspired by biological evolution are frequently applied to generate autonomous agents too complex to design by hand. Despite substantial progress in the area of evolutionary computation, additional efforts are needed to identify a coherent set of requirements for a system capable of exhibiting open-ended evolutionary dynamics. The thesis provides an extensive discussion of existing models and of the major considerations for designing a computational model of evolution by natural selection. Thus, the work in this thesis constitutes a further step towards determining the requirements for such a system and introduces a concrete implementation of an artificial evolution system to evaluate the developed suggestions. The proposed system improves upon existing models with respect to easy interpretability of agent behaviour, high structural freedom, and a low-level sensor and effector model to allow numerous long-term evolutionary gradients. In a series of experiments, the evolutionary dynamics of the system are examined against the set objectives and, where appropriate, compared with existing systems. Typical agent behaviours are introduced to convey a general overview of the system dynamics. These behaviours are related to properties of the respective agent populations and their evolved morphologies. It is shown that an intuitive classification of observed behaviours coincides with a more formal classification based on morphology. The evolutionary dynamics of the system are evaluated and shown to be unbounded according to the classification provided by Bedau and Packard’s measures of evolutionary activity. Further, it is analysed how observed behavioural complexity relates to the complexity of the agent-side mechanisms subserving these behaviours. It is shown that for the concrete definition of complexity applied, the average complexity continually increases for extended periods of evolutionary time. In combination, these two findings show how the observed behaviours are the result of an ongoing and lasting adaptive evolutionary process as opposed to being artifacts of the seeding process. Finally, the effect of variation in the system on the diversity of evolved behaviour is investigated. It is shown that coupling individual survival and reproductive success can restrict the available evolutionary trajectories in more than the trivial sense of removing another dimension, and conversely, decoupling individual survival from reproductive success can increase the number of evolutionary trajectories. The effect of different reproductive mechanisms is contrasted with that of variation in environmental conditions. The diversity of evolved strategies turns out to be sensitive to the reproductive mechanism while being remarkably robust to the variation of environmental conditions. These findings emphasize the importance of being explicit about the abstractions and assumptions underlying an artificial evolution system, particularly if the system is intended to model aspects of biological evolution

Sensing bodies:Transdisciplinary enactments of ‘thing-power’ and ‘making-with’ for educational future-making.

Dominant conceptions of education are strongly framed by narratives of ‘power-over’ materials, context, and processes, especially where digital and technological applications reduce complexities between humans, materials, and environments. The separation of knowledge, tools, and bodies in ‘disciplinary bounded’, ‘copyrighted’, and ‘patented’ spaces create a disconnect from our need for sustainable relationships, whereby the future is not given but ‘in-the-making’ (Haraway 2016). Drawing on music and science – as examples of distinct disciplines, often siloed and separated in education – this paper advances nuanced understandings of how post human conceptions of ‘thing-power’1(the power of all bodies including materials) and ‘making-with’ (whereby everything makes each other capable) contribute to the affective encounters of materialities within the classroom. By foregrounding the sensing body as a means to touch and be ‘touched’ by the world, we uniquely contribute to methodologies that illuminate the relational intensity of material sensation as part of coming to ‘know’. In doing so, we engage with the performative work of these materialities and re-define the ‘digital’ beyond the delivery of preplanned learning pathways

Tandem Mass Spectrometric and Ion Mobility Studies of Supramolecular Complexes

Synthetic supramolecular systems share many similarities with natural biological assemblies, especially when considering that the structure and guest binding are typically governed by non-covalent interactions. As such, the defining characteristic is that only comparably weak forces define the shape of a synthetic supramolecule or the tertiary structure of a protein, so that the resulting dynamic binding mode makes structure elucidation challenging. One of the major advances in recent analytical chemistry has been the development of ion mobility-mass spectrometry (IM-MS) to tackle the challenging problems faced in proteomics, glycomics, metabolomics, and lipidomics. By analogy, the prospects of applying IM-MS to supramolecules are bright and it is to be expected that unprecedented analytical insights into diverse systems such as host-guest complexes, molecular devices, self-assemblies and metallosupramolecular complexes will be obtained. The recurrent theme throughout this dissertation is that both structure (differentiation of diastereomers, photoisomers, mechanoisomers) and non-covalent interactions (hydrogen bonding, $TTF^{n+}/TTF^{n+}$-charge repulsion, dispersive interactions) can be investigated by a combination of the three methods of ion-mobility mass spectrometry (IM-MS), collision-induced dissociation (CID) and gas-phase H/D-exchange (GP-HDX). In the study of the gas-phase chiral recognition of crown-ether ammonium complexes, the importance of a single hydrogen bond for the enantiodifferentiation was revealed. Similarly, in an azobenzene model a hydrogen bonding interaction led to an increased stability of the (Z)-photoisomer. This surprising observation illustrates an important aspect, namely that there can be significant differences between the gas-phase and the solution environment. In the absence of solvent, both the stabilization of charged sites and the Coulomb repulsion of nearby charges are accentuated. In a way, the conundrum of supramolecular mass spectrometry revolves around the problem that ions are easily manipulated in the gas-phase where a high analytic resolution power is available, to then face the question if the obtained results still reflect the solution environment. Therefore, it is very convincing to see that in three of the five presented studies, the solution environment is reflected in a quantitative fashion: In the quantification of the enantiomeric excess (first study), the quantification of photoisomer content (second study), and the quantitative determination of equilibrium constants for redox-controlled dethreading (third study). Together with these five studies, and the detailed description in the subsequent chapters, I expect the treatment to be useful also from the practitioner's point of view. It is my hope that the performance, speed, and reliability with which measurements can be performed with modern instrumentation will make IM-MS a routine analytical tool in the repertoire of the working supramolecular chemist

The Translocal Event and the Polyrhythmic Diagram

This thesis identifies and analyses the key creative protocols in translocal performance practice, and ends with suggestions for new forms of transversal live and mediated performance practice, informed by theory. It argues that ontologies of emergence in dynamic systems nourish contemporary practice in the digital arts. Feedback in self-organised, recursive systems and organisms elicit change, and change transforms. The arguments trace concepts from chaos and complexity theory to virtual multiplicity, relationality, intuition and individuation (in the work of Bergson, Deleuze, Guattari, Simondon, Massumi, and other process theorists). It then examines the intersection of methodologies in philosophy, science and art and the radical contingencies implicit in the technicity of real-time, collaborative composition. Simultaneous forces or tendencies such as perception/memory, content/ expression and instinct/intellect produce composites (experience, meaning, and intuition- respectively) that affect the sensation of interplay. The translocal event is itself a diagram - an interstice between the forces of the local and the global, between the tendencies of the individual and the collective. The translocal is a point of reference for exploring the distribution of affect, parameters of control and emergent aesthetics. Translocal interplay, enabled by digital technologies and network protocols, is ontogenetic and autopoietic; diagrammatic and synaesthetic; intuitive and transductive. KeyWorx is a software application developed for realtime, distributed, multimodal media processing. As a technological tool created by artists, KeyWorx supports this intuitive type of creative experience: a real-time, translocal “jamming” that transduces the lived experience of a “biogram,” a synaesthetic hinge-dimension. The emerging aesthetics are processual – intuitive, diagrammatic and transversal