A Note of Zipf's Law, Natural Languages, and Noncoding DNA Regions

In Phys. Rev. Letters (73:2), Mantegna et al. conclude on the basis of Zipf rank frequency data that noncoding DNA sequence regions are more like natural languages than coding regions. We argue on the contrary that an empirical fit to Zipf"s "law" cannot be used as a criterion for similarity to natural languages. Although DNA is a presumably "organized system of signs" in Mandelbrot"s (1961) sense, and observation of statistical featurs of the sort presented in the Mantegna et al. paper does not shed light on the similarity between DNA's "gramar" and natural language grammars, just as the observation of exact Zipf-like behavior cannot distinguish between the underlying processes of tossing an M-sided die or a finite-state branching process.

Specialization of Perceptual Processes

In this report, I discuss the use of vision to support concrete, everyday activity. I will argue that a variety of interesting tasks can be solved using simple and inexpensive vision systems. I will provide a number of working examples in the form of a state-of-the-art mobile robot, Polly, which uses vision to give primitive tours of the seventh floor of the MIT AI Laboratory. By current standards, the robot has a broad behavioral repertoire and is both simple and inexpensive (the complete robot was built for less than $20,000 using commercial board-level components). The approach I will use will be to treat the structure of the agent's activity---its task and environment---as positive resources for the vision system designer. By performing a careful analysis of task and environment, the designer can determine a broad space of mechanisms which can perform the desired activity. My principal thesis is that for a broad range of activities, the space of applicable mechanisms will be broad enough to include a number mechanisms which are simple and economical. The simplest mechanisms that solve a given problem will typically be quite specialized to that problem. One thus worries that building simple vision systems will be require a great deal of {it ad-hoc} engineering that cannot be transferred to other problems. My second thesis is that specialized systems can be analyzed and understood in a principled manner, one that allows general lessons to be extracted from specialized systems. I will present a general approach to analyzing specialization through the use of transformations that provably improve performance. By demonstrating a sequence of transformations that derive a specialized system from a more general one, we can summarize the specialization of the former in a compact form that makes explicit the additional assumptions that it makes about its environment. The summary can be used to predict the performance of the system in novel environments. Individual transformations can be recycled in the design of future systems.

Using an Outdoor Learning Space to Teach Sustainability and Material Processes in HE product Design.

The world is facing environmental changes that are increasingly affecting how we think about manufacturing, the consumption of products and use of resources. Within the HE product design community, thinking and designing sustainability’ has evolved to become a natural part of the curriculum. Paradoxical as the rise in awareness of sustainability increases there is growing concern within HE product design of the loss of workshop facilities and as a consequence a demise in teaching traditional object-making skills and material experimentation. We suggest the loss of workshops and tangible ‘learning by making skills’ also creates a lost opportunity for a rich learning resource to address sustainable thinking, design and manufacture ‘praxis’ within HE design education. Furthermore, as learning spaces are frequently discussed in design research, there seems to be little focus on how the use of an outdoor environment might influence learning outcomes particularly with regard to material teaching and sustainability. This 'case study' of two jewellery workshops, used outdoor learning spaces to explore both its impact on learning outcomes and to introduce some key principles of sustainable working methodologies and practices. Academics and students mainly from Norway and Scotland collaborated on this international research project. Participants made models from disposable packaging materials, which were cast in tin, in the sand on a local beach, using found timber to create a heat source for melting the metal. This approach of using traditional making skills, materials and nature was found to be a relevant contribution to a sustainable discourse.

Modelling random fuzzy renewal reward processes

Shen, Q., Zhao, R., Tang, W. (2008). Modelling random fuzzy renewal reward processes. IEEE Transactions on Fuzzy Systems, 16 (5),1379-1385

Electrons in feldspar II: a consideration of the influence of conduction band-tail states on luminescence processes

Poolton, Nigel; Ozanyan, K.B.; Wallinga, J.; Murray, A.S., (2002) 'Electrons in feldspar II: a consideration of the influence of conduction band-tail states on luminescence processes', Physics and Chemistry of Minerals 29(3) pp.217-225 RAE2008

Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes

BACKGROUND:Recent advances in genome sequencing suggest a remarkable conservation in gene content of mammalian organisms. The similarity in gene repertoire present in different organisms has increased interest in studying regulatory mechanisms of gene expression aimed at elucidating the differences in phenotypes. In particular, a proximal promoter region contains a large number of regulatory elements that control the expression of its downstream gene. Although many studies have focused on identification of these elements, a broader picture on the complexity of transcriptional regulation of different biological processes has not been addressed in mammals. The regulatory complexity may strongly correlate with gene function, as different evolutionary forces must act on the regulatory systems under different biological conditions. We investigate this hypothesis by comparing the conservation of promoters upstream of genes classified in different functional categories.RESULTS:By conducting a rank correlation analysis between functional annotation and upstream sequence alignment scores obtained by human-mouse and human-dog comparison, we found a significantly greater conservation of the upstream sequence of genes involved in development, cell communication, neural functions and signaling processes than those involved in more basic processes shared with unicellular organisms such as metabolism and ribosomal function. This observation persists after controlling for G+C content. Considering conservation as a functional signature, we hypothesize a higher density of cis-regulatory elements upstream of genes participating in complex and adaptive processes.CONCLUSION:We identified a class of functions that are associated with either high or low promoter conservation in mammals. We detected a significant tendency that points to complex and adaptive processes were associated with higher promoter conservation, despite the fact that they have emerged relatively recently during evolution. We described and contrasted several hypotheses that provide a deeper insight into how transcriptional complexity might have been emerged during evolution.

Conversion as transformative experience: a sociological study of identity formation and transformation processes

This thesis contributes to the understanding of the processes involved in the formation and transformation of identities. It achieves this goal by establishing the critical importance of ‘background’ and ‘liminality’ in the shaping of identity. Drawing mainly from the work of cultural anthropology and philosophical hermeneutics a theoretical framework is constructed from which transformative experiences can be analysed. The particular experience at the heart of this study is the phenomenon of conversion and the dynamics involved in the construction of that process. Establishing the axial age as the horizon from which the process of conversion emerged will be the main theme of the first part of the study. Identifying the ‘birth’ of conversion allows a deeper understanding of the historical dynamics that make up the process. From these fundamental dynamics a theoretical framework is constructed in order to analyse the conversion process. Applying this theoretical framework to a number of case-studies will be the central focus of this study. The transformative experiences of Saint Augustine, the fourteenth century nun Margaret Ebner, the communist revolutionary Karl Marx and the literary figure of Arthur Koestler will provide the material onto which the theoretical framework can be applied. A synthesis of the Judaic religious and the Greek philosophical traditions will be the main findings for the shaping of Augustine’s conversion experience. The dissolution of political order coupled with the institutionalisation of the conversion process will illuminate the mystical experiences of Margaret Ebner at a time when empathetic conversion reached its fullest expression. The final case-studies examine two modern ‘conversions’ that seem to have an ideological rather than a religious basis to them. On closer examination it will be found that the German tradition of Biblical Criticism played a most influential role in the ‘conversion’ of Marx and mythology the best medium to understand the experiences of Koestler. The main ideas emerging from this study highlight the fluidity of identity and the important role of ‘background’ in its transformation. The theoretical framework, as constructed for this study, is found to be a useful methodological tool that can offer insights into experiences, such as conversion, that otherwise would remain hidden from our enquiries.

Optimisation of chemoenzymatic processes in asymmetric synthesis

This thesis describes the optimisation of chemoenzymatic methods in asymmetric synthesis. Modern synthetic organic chemistry has experienced an enormous growth in biocatalytic methodologies; enzymatic transformations and whole cell bioconversions have become generally accepted synthetic tools for asymmetric synthesis. Biocatalysts are exceptional catalysts, combining broad substrate scope with high regio-, enantio- and chemoselectivities enabling the resolution of organic substrates with superb efficiency and selectivity. In this study three biocatalytic applications in enantioselective synthesis were explored and perhaps the most significant outcome of this work is the excellent enantioselectivity achieved through optimisation of reaction conditions improving the synthetic utility of the biotransformations. In the first chapter a summary of literature discussing the stereochemical control of baker’s yeast (Saccharomyces Cerevisae) mediated reduction of ketones by the introduction of sulfur moieties is presented, and sets the work of Chapter 2 in context. The focus of the second chapter was the synthesis and biocatalytic resolution of (±)-trans-2-benzenesulfonyl-3-n-butylcyclopentanone. For the first time the practical limitations of this resolution have been addressed providing synthetically useful quantities of enantiopure synthons for application in the total synthesis of both enantiomers of 4-methyloctanoic acid, the aggregation pheromone of the rhinoceros beetles of the genus Oryctes. The unique aspect of this enantioselective synthesis was the overall regio- and enantioselective introduction of the methyl group to the octanoic acid chain. This work is part of an ongoing research programme in our group focussed on baker’s yeast mediated kinetic resolution of 2-keto sulfones. The third chapter describes hydrolase-catalysed kinetic resolutions leading to a series of 3-aryl alkanoic acids. Hydrolysis of the ethyl esters with a series of hydrolases was undertaken to identify biocatalysts that yield the corresponding acids in highly enantioenriched form. Contrary to literature reports where a complete disappearance of efficiency and, accordingly enantioselection, was described upon kinetic resolution of sterically demanding 3-arylalkanoic acids, the highest reported enantiopurities of these acids was achieved (up to >98% ee) in this study through optimisation of reaction conditions. Steric and electronic effects on the efficiency and enantioselectivity of the biocatalytic transformation were also explored. Furthermore, a novel approach to determine the absolute stereochemistry of the enantiopure 3-aryl alkanoic acids was investigated through combination of co-crystallisation and X-ray diffraction linked with chiral HPLC analysis. The fourth chapter was focused on the development of a biocatalytic protocol for the asymmetric Henry reaction. Efficient kinetic resolution in hydrolase-mediated transesterification of cis- and trans- β-nitrocyclohexanol derivatives was achieved. Combination of a base-catalysed intramolecular Henry reaction coupled with the hydrolase-mediated kinetic resolution with the view to selective acetylation of a single stereoisomer was investigated. While dynamic kinetic resolution in the intramolecular Henry was not achieved, significant progress in each of the individual elements was made and significantly the feasibility of this process has been demonstrated. The final chapter contains the full experimental details, including spectroscopic and analytical data of all compounds synthesised in this project, while details of chiral HPLC analysis are included in the appendix. The data for the crystal structures are contained in the attached CD.