Ed. D.

This thesis presents an investigation into developing musical systems with an Unconventional Computing substrate. Computer musicians have found it difficult to access the field of Unconventional Computing, which is likely due to its resource-intensive and complex nature. However, ongoing research is establishing the myxomycete Physarum polycephalum as a universally-accessible and versatile biological computing substrate. As such, the organism is a potential gateway for computer musicians to begin experimenting with aspects of Unconventional Computing. Physarum polycephalum, in its vegetative plasmodium form, is an amorphous unicellular organism that can respond with natural parallelism to the environmental conditions that surround it. This thesis explores the challenges and opportunities related to developing musical systems with Physarum polycephalum. As this area of inquiry is in its infancy, the research took inspiration from a common approach in Unconventional Computing: a journey of exploration and discovery. This journey consisted of a selection of waypoints that provided direction while allowing the research to explore applications of Physarum polycephalum in order to establish how it may be useful in Computer Music. These waypoints guided the research from adapting established prototypes for musical application to developing purpose-made musical demonstrators for use outside of the laboratory. Thus, the thesis reports on a series of Computer Music systems that explore one or more features of Physarum polycephalum's behaviour and physiology. First, the text presents an approach to algorithmic composition that exploits the organism's ability to form and reconfigure graph-like structures. Next, the thesis reports on systems that harness the plasmodium's electrical potential oscillations for sound synthesis and compositional tools. Finally, the thesis presents musical devices that encompass living plasmodium as electrical components. Where applicable, the thesis includes artefacts from demonstrations of these systems, some of which were developed in collaboration with a composer. The findings from this journey demonstrate that Physarum polycephalum is an appropriate substrate for computer musicians wanting to explore Unconventional Computing approaches creatively. Although Physarum polycephalum is relatively robust as a biological substrate, several obstacles arose during this project. This research addressed such obstacles by reviewing and selecting approaches that maintained the organism's accessibility to computer musicians. As a result, the work suggests methods for developing systems with the organism that are practical for the average music technologist and also beneficial to the wider group of scientists investigating Physarum polycephalum for other purposes.

Un des domaines clés de l’étude du comportement animal s’intéresse aux différents moyens par lesquels les individus obtiennent et utilisent l’information de leur environnement. Ces études permettent de comprendre les stimuli responsables de la modulation des réponses comportementales des organismes et d’appréhender comment des individus interagissent. L’importance écologique des organismes unicellulaires n’étant plus à prouver, une compréhension de leurs capacités à percevoir l’environnement, aussi bien biotique que abiotique, semble primordiale. Ainsi, nous avons étudié l’aptitude d’un organisme unicellulaire (Physarum polycephalum) à percevoir et utiliser l’information dans différents contextes. Cette thèse s’articule autour de cinq articles dans lesquels nous présentons nos résultats obtenus en utilisant les outils d’étude du comportement animal pour analyser et quantifier les comportements de cet organisme unicellulaire. Nous démontrons que Physarum polycephalum possède des traits comportementaux semblables aux organismes plus complexe : comme la communication, la coopération, la variabilité phénotypique et l’apprentissage. Nos résultats suggèrent l’importance de l’étude du comportement des organismes unicellulaires dans la compréhension de différents mécanismes biologiques. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

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Empirical studies show that similar patterns emerge from a large number of different biological systems. For example, the group size distributions of several fish species and house sparrows all follow power law distributions with an exponential truncation. Networks built by ant colonies, slime mold and those are designed by engineers resemble each other in terms of structure and transportation efficiency. Based on the investigation of experimental data, we propose a variety of simple stochastic models to unravel the underlying mechanisms which lead to the collective phenomena in different systems. All the mechanisms employed in these models are rooted in the concept of selective reinforcement. In some systems the reinforcement can build optimal solutions for biological problem solving. This thesis consists of five papers. In the first three papers, I collaborate with biologists to look into group formation in house sparrows  and the movement decisions of damsel fish.  In the last two articles, I look at how shortest paths and networks are  constructed by slime molds and pheromone laying ants, as well as studying  speed-accuracy tradeoffs in slime molds' decision making. The general goal of the study is to better understand how macro level patterns and behaviors emerges from micro level interactions in both spatial and non-spatial biological systems. With the combination of mathematical modeling and experimentation, we are able to reproduce the macro level patterns in the studied biological systems and predict behaviors of the systems using minimum number of parameters.

The study of landscape structure and configuration is firmly established as integral to the continued advancement of ecology. The configuration of resource patches can have far-reaching implications for biodiversity, metapopulation dynamics, community structure, and habitat quality. Human activities, such as forestry, agriculture, and residential construction alter patch configuration by breaking larger patches into smaller fragments. This frequently results in pronounced, unforeseen consequences for species. The fragmentation and shrinking of habitat patches can lead to changes in the environmental conditions within the remaining patches (e.g., degradation), prompting responses from local populations. These responses can, in turn, cause changes to the metapopulation structure on large spatial scale.<br>I examined the relationship between the degree of habitat fragmentation (edge density), and forewing lengths of the ebony jewelwing damselfly (Calopteryx maculata Beauvois, Odonata: Calopterygidae). I used correlated random walks to determine the biologically relevant landscape area over which forest fragmentation was calculated. Then, I used Moran’s I to determine the spatial scale of wing length response to fragmentation. I found that wing lengths increased with edge density. I also found that wing lengths were spatially autocorrelated at distances below 5 Km. These findings suggest that damselflies adapt to changes in forest fragmentation at a relatively small spatial scale.<br>Next, I assessed the slime mold Physarum polycephalum’s usefulness as a microcosm of dispersal in fragmented landscapes. Slime mold plasmodia were placed in dishes with oat patches of varying sizes and distances. The probability of each patch type being colonized first was compared to predictions of patch occupancy based on C. maculata. Patches that were nearer or larger were likely to be colonized before patches that were more distant, or smaller. Observed patch occupancy matched model predictions when only patch distance was varied, but not when patch size was varied. These results suggest that P. polycephalum has the potential to serve as a useful microcosm of dispersal in patchy landscapes. However, more testing is needed to develop the microcosm system. <br>Finally, a lesson plan was developed to teach high school students about the concepts of landscape ecology and connectivity. An emphasis was placed on using active learning techniques, which have been demonstrated to result in greater understanding than traditional lecture formats. The lesson plan incorporates an education boardgame, Humans & Habitats, that I developed to illustrate how the conflicting goals of resource managers impact habitat connectivity. It also incorporates a scientific inquiry activity that uses P. polycephalum to test predictions about the effect of altered connectivity. The lesson plan and materials will be available to members of the public, free of charge.<br><br>