京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第19000号 / 工博第4042号 / 新制||工||1622(附属図書館) / 31951 / 京都大学大学院工学研究科分子工学専攻 / (主査)教授 田中 庸裕, 教授 今堀 博, 教授 阿部 竜 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

<p>The interest for cooperative robots has increased considerably in recent years and one of the research issues within this domain is how to evolve heterogeneity in a team. The research today is however either focusing on diversity in hardware (e.g. sensory system) or diversity of behaviour. This dissertation extends this research and presents experiments that attempts to 'co-evolve' heterogeneity at both the hardware level and the behavioural level. The results show that the team behaviour evolved depends on the complexity of the task where adding constraints or increasing the difficulty of the problem lead to better team behaviour.</p><p>Our belief was that the performance of the team should benefit from using robots that has been evolved at the hardware level together with the behavioural level. This, however, could not be proved to be true, but the idea that these two should be kept together in order to evolve heterogeneity in a team is still believed.</p>

The interest for cooperative robots has increased considerably in recent years and one of the research issues within this domain is how to evolve heterogeneity in a team. The research today is however either focusing on diversity in hardware (e.g. sensory system) or diversity of behaviour. This dissertation extends this research and presents experiments that attempts to 'co-evolve' heterogeneity at both the hardware level and the behavioural level. The results show that the team behaviour evolved depends on the complexity of the task where adding constraints or increasing the difficulty of the problem lead to better team behaviour. Our belief was that the performance of the team should benefit from using robots that has been evolved at the hardware level together with the behavioural level. This, however, could not be proved to be true, but the idea that these two should be kept together in order to evolve heterogeneity in a team is still believed.

<p>A recent trend in evolutionary robotics and artificial life research is to maximize self-organization in the design of robotic systems, in particular using artificial evolutionary techniques, in order to reduce the human designer bias. This dissertation presents experiments in competitive co-evolutionary robotics that integrate and extend previous work on competitive co-evolution of neural robot controllers in a predator-prey scenario with work on the ‘co-evolution’ of robot morphology and control systems. The focus here is on a systematic investigation of tradeoffs and interdependencies between morphological parameters and behavioral strategies through a series of predator-prey experiments in which increasingly many aspects are subject to self-organization through competitive co-evolution. The results show that there is a strong interdependency between morphological parameters and behavioral strategies evolved, and that the competitive co-evolutionary process was able to find a balance between and within these two aspects. It is therefore concluded that competitive co-evolution has great potential as a method for the automatic design of robotic systems.</p>

A recent trend in evolutionary robotics and artificial life research is to maximize self-organization in the design of robotic systems, in particular using artificial evolutionary techniques, in order to reduce the human designer bias. This dissertation presents experiments in competitive co-evolutionary robotics that integrate and extend previous work on competitive co-evolution of neural robot controllers in a predator-prey scenario with work on the ‘co-evolution’ of robot morphology and control systems. The focus here is on a systematic investigation of tradeoffs and interdependencies between morphological parameters and behavioral strategies through a series of predator-prey experiments in which increasingly many aspects are subject to self-organization through competitive co-evolution. The results show that there is a strong interdependency between morphological parameters and behavioral strategies evolved, and that the competitive co-evolutionary process was able to find a balance between and within these two aspects. It is therefore concluded that competitive co-evolution has great potential as a method for the automatic design of robotic systems.

Software developers adapt to the fast-moving nature of software systems with agile development techniques. However, database developers lack the tools and concepts to keep the pace. Whenever the current database schema is evolved, the already existing data needs to be evolved as well. This is usually realized with manually written SQL scripts, which is error-prone and explains significant costs in software projects. A promising solution are declarative database evolution languages, which couple both schema and data evolution into intuitive operations. Existing database evolution languages focus on usability but do not strive for completeness. However, this is an inevitable prerequisite to avoid complex and error-prone workarounds. We present CODEL which is based on an existing language but is relationally complete. We precisely define its semantic using relational algebra, propose a syntax, and formally validate its relational completeness. Having a complete and comprehensive database evolution language facilitates valuable support throughout the whole evolution of a database. As an instance, we present VACO, a tool supporting developers with variant co-evolution. Given a variant schema derived from a core schema, VACO uses the richer semantics of CODEL to semi-automatically co-evolve this variant with the core.

Viruses are the most abundant biological entity on Earth and outnumber their hosts ten-to-one. Ocean viruses (phages) impact bacterial-driven global biogeochemical cycles through lysis, manipulating host metabolism, and horizontal gene transfer. However, knowledge of virus-host interactions and viral roles in ecosystems remains limited due to few cultured marine phage genomes and non-quantitative culture-independent metagenomes. Here, I develop and apply novel and well-tested bioinformatic techniques to explore Pacific Ocean viral communities using quantitative datasets derived from rigorously-tested preparation methods. To evaluate concentration and purification methods, I examined triplicate metagenomes from a single ocean sample using four protocols. Concentration protocols showed statistical differences in taxonomy whereas purification protocols did not. Specifically, TFF-concentrated metagenomes contained trace bacterial contamination and had fewer abundant taxa as compared to FeCl₃-precipitated metagenomes. K-mer analysis using the complete dataset revealed polymerase choice defined access to "rare" sequences.To explore unknown viral sequences, I organized known and unknown sequence space into 27K high-confidence protein clusters (PCs) from 32 diverse Pacific Ocean Virus (POV) metagenomes, which doubled available PCs and included the first pelagic deep-sea viral metagenomes. Using PCs as a whole-viral-community diversity metric revealed decreases from coastal to open ocean, winter to summer, and deep to surface, that correlate with data from microbial genetic diversity markers (no parallel viral markers exist).Biologically, POV metagenomes showed that viruses likely reprogram central metabolic pathways in microbial communities far beyond the "photosynthesis viruses" paradigm. Gene distribution patterns from 35 viral gene families (31 new) revealed niche-specific (photic vs aphotic zone) altered pathway carbon flux presumably optimized to best locally generate energy and drive viral replication. Further, these PCs define the first "core" (180 genes) and "flexible" (423K genes total) viral community genome. Functionally, core genes again suggest niche-differentation with extensive Fe-S cluster-related genes for electron transport and metabolic enzyme catalysis in photic samples, and manipulation of host pressure-sensitive genes in aphotic samples. Taxonomically, these data deconstruct the culture-based paradigm that tailed viruses dominate in the wild - instead they appear ubiquitous, but not abundant.

本論文旨在分析法國法蘭西研究院院士Michel Serres的思想及其在教育上的啟思。Michel Serres是一名著名的法國哲學家，但是在台灣他還是一名較不為人所熟知的學者。然而經過本論文對於其思想進行研究，發現其理論有許多重要的教育哲學思想。因此，本論文首先便由Serres的法文原著，探究他的理論定位及其思維特色。而後，本論文以「吟遊、尋渡與參化」之三向度作為分析的軸心，來探討Serres的理論在教育上的重要涵意：在吟遊的層面上，吟遊當中的旅程、漂流、孤獨、暴露、受苦、節制、愛、與創造等概念，蘊含的是Serres的教育人類學的想像；在尋渡的層面上，由於吟遊者在漂流中去執、受苦、節制、愛與創造，因此他將不斷轉化自身，也將不斷地在知識與知識之間，以及人於人之間尋找交融之渡，這蘊含的是Serres的教育倫理學的想像；而在參化的層面上，除了投入人群，吟遊者將轉化自身，投入自然以及萬事萬物之中，與人、與自然以及萬事萬物相互參化，這蘊含的是Serres的教育美學的想像。「吟遊、尋渡與參化」，這三者就是Serres對於「教育」這一概念的開展與想像。 / This study is to investigate the thought and implication for education of Michel Serres, a distinct member of L'Académie française. Michel Serres is a famous philosopher, but he is not well-known in Taiwan. Through examining Serres’s thought, we can find many inspiring ideas of educational philosophy. In the first part of this dissertation, it will focus on Serres’s original French texts in order to explore the orientation and the characteristic of his theories. Secondly, this dissertation will discuss the critical three axes of Serres’s theories: ‘Troubadour, Seeking Passage and Co-evolution.’ Troubadour entails the ideas of voyage, érrance (wanderings), solitude, expose to, suffering, temperance, love, and creation. These concepts imply the image of Serres’s educational anthropology. Seeking passage indicates the self-detachment, suffering, temperance, love, and creation of Troubadour. Because of érrance, Troubadour will never stop self-transforming and will constantly searching for the passages among different knowledge as well as the passages among people. This implies the image of Serres’s educational ethics. Co-evolution represents Troubadour’s engagement not only in human beings but also in nature and in all things on earth because of his self-transformation. The troubadour eagerly engages himself in the co-evolution with other human beings, nature and all things on earth. This implies the image of Serres’s educational esthetics. The ideas of ‘Troubadour, Seeking Passage and Co-evolution’ are the keystones of Serres’s discourses and images on education.

Parasite documentation has been an important tool to understand host history and co-evolutionary processes in these associations. Acanthobothrium is a worldwide genus of cestodes, and it is a parasite of sharks, skates and rays, with almost 200 nominal species. Recent studies are presenting new hypotheses on cestodes distribution and host specificity patterns. Due to their large distribution, geographical and in host taxa, Acanthobothrium seems to be a good model to evaluate these hypothesis. The Bay of Marajó is an estuarine area were freshwater stingrays of the family Potamotrygonidae share the same environment with marine dasyatid rays. There is no documentation about the dasyatid fauna of Acanthobothrium for Bay of Marajó, neither their relationships with freshwater lineages or their hosts. In our goal to understand those evolutionary events, our results revealed six new lineages of Acanthobothrium, parasites of Hypanus guttatus and Fontitrygon geijskesi, of which four are formally described. Five of those new lineages are included in a clade exclusive to Northwest Atlantic and Caribbean Sea. Acanthobothrium sp. 10 was recovered as sister of clade formed by marine Acanthobothrium sp. 9 sensu Trevisan and freshwater Acanthobothrium sp. 2 sensu Cardoso Jr. The specificity pattern of Acanthobothrium has been discussed and our results corroborate this discussion when we observed four species of Acanthobothrium sharing two different hosts of different genera. Also, host sample size may be correlated with the specificity and strict specificity patterns of the parasite to their hosts. The absence of Fontitrygon colarensis in our samples and the incongruities in comparison to Hypanus guttatus make us question the taxonomic status of F. Colarensis / A documentação de organismos parasitas tem sido uma ferramenta importante para entender a história de seus hospedeiros e os processos coevolutivos implícitos nessas associações. Acanthobothrium é um gênero de cestóideos mundialmente distribuido, parasita de tubarões, skates e raias, com quase 200 espécies nominais. Estudos recentes vem apresentando novas hipóteses sobre a distribuição e especificidade dos cestóides. Devido à sua larga distribuição geográfica e em taxons hospedeiros, Acanthobothrium parece ser um bom modelo para avaliar estas hipóteses. A Baía de Marajó é uma área estuarina onde arraias de água doce da família Potamotrygonidae compartilham o mesmo ambiente com raias marinhas, especialmente dasiatídeos. Não há documentação sobre a fauna de Dasyatidae para Acanthobothrium a Baía de Marajó, nem sobre as relações destas com linhagens de água doce e seus hospedeiros. Com o objetivo de entender esses eventos evolutivos, nossos resultados mostraram seis novas linhagens de Acanthobothrium, parasitas de Hypanus guttatus e Fontitrygon geijskesi, das quais quatro são descritas. Cinco dessas novas linhagens estão incluídas em um clado exclusivamente do Noroeste Atlântico e do Mar do Caribe. Acanthobothrium sp. 10 foi recuperado como grupo irmão de um clado formado pela linhagem marinha Acanthobothrium sp. 9 sensu Trevisan e pela linhagem de água doce Acanthobothrium sp. 2 sensu Cardoso Jr. O padrão de especificidade de Acanthobothrium tem sido discutido e nossos resultados corroboram esta discussão quando observamos quatro espécies de Acanthobothrium compartilhando duas hospedeiras de diferentes gêneros. Além disso, tamanho amostral de hospedeiros pode estar relacionado com nosso entendimento sobre os padrões de especificidade estrita do parasita aos seus hospedeiros. A ausência de F. Colarensis em nossas amostras e as incongruências em comparação com H. Guttatus nos fazem questionar o status taxonômico de F. Colarensis

Parasite documentation has been an important tool to understand host history and co-evolutionary processes in these associations. Acanthobothrium is a worldwide genus of cestodes, and it is a parasite of sharks, skates and rays, with almost 200 nominal species. Recent studies are presenting new hypotheses on cestodes distribution and host specificity patterns. Due to their large distribution, geographical and in host taxa, Acanthobothrium seems to be a good model to evaluate these hypothesis. The Bay of Marajó is an estuarine area were freshwater stingrays of the family Potamotrygonidae share the same environment with marine dasyatid rays. There is no documentation about the dasyatid fauna of Acanthobothrium for Bay of Marajó, neither their relationships with freshwater lineages or their hosts. In our goal to understand those evolutionary events, our results revealed six new lineages of Acanthobothrium, parasites of Hypanus guttatus and Fontitrygon geijskesi, of which four are formally described. Five of those new lineages are included in a clade exclusive to Northwest Atlantic and Caribbean Sea. Acanthobothrium sp. 10 was recovered as sister of clade formed by marine Acanthobothrium sp. 9 sensu Trevisan and freshwater Acanthobothrium sp. 2 sensu Cardoso Jr. The specificity pattern of Acanthobothrium has been discussed and our results corroborate this discussion when we observed four species of Acanthobothrium sharing two different hosts of different genera. Also, host sample size may be correlated with the specificity and strict specificity patterns of the parasite to their hosts. The absence of Fontitrygon colarensis in our samples and the incongruities in comparison to Hypanus guttatus make us question the taxonomic status of F. Colarensis / A documentação de organismos parasitas tem sido uma ferramenta importante para entender a história de seus hospedeiros e os processos coevolutivos implícitos nessas associações. Acanthobothrium é um gênero de cestóideos mundialmente distribuido, parasita de tubarões, skates e raias, com quase 200 espécies nominais. Estudos recentes vem apresentando novas hipóteses sobre a distribuição e especificidade dos cestóides. Devido à sua larga distribuição geográfica e em taxons hospedeiros, Acanthobothrium parece ser um bom modelo para avaliar estas hipóteses. A Baía de Marajó é uma área estuarina onde arraias de água doce da família Potamotrygonidae compartilham o mesmo ambiente com raias marinhas, especialmente dasiatídeos. Não há documentação sobre a fauna de Dasyatidae para Acanthobothrium a Baía de Marajó, nem sobre as relações destas com linhagens de água doce e seus hospedeiros. Com o objetivo de entender esses eventos evolutivos, nossos resultados mostraram seis novas linhagens de Acanthobothrium, parasitas de Hypanus guttatus e Fontitrygon geijskesi, das quais quatro são descritas. Cinco dessas novas linhagens estão incluídas em um clado exclusivamente do Noroeste Atlântico e do Mar do Caribe. Acanthobothrium sp. 10 foi recuperado como grupo irmão de um clado formado pela linhagem marinha Acanthobothrium sp. 9 sensu Trevisan e pela linhagem de água doce Acanthobothrium sp. 2 sensu Cardoso Jr. O padrão de especificidade de Acanthobothrium tem sido discutido e nossos resultados corroboram esta discussão quando observamos quatro espécies de Acanthobothrium compartilhando duas hospedeiras de diferentes gêneros. Além disso, tamanho amostral de hospedeiros pode estar relacionado com nosso entendimento sobre os padrões de especificidade estrita do parasita aos seus hospedeiros. A ausência de F. Colarensis em nossas amostras e as incongruências em comparação com H. Guttatus nos fazem questionar o status taxonômico de F. Colarensis