Transcription factor motif quality assessment requires systematic comparative analysis [version 2; referees: 2 approved]
- Kibet, Caleb K, Machanick, Philip
- Authors: Kibet, Caleb K , Machanick, Philip
- Date: 2016
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/61169 , vital:27987 , http://dx.doi.org/10.12688/f1000research.7408.2
- Description: Transcription factor (TF) binding site prediction remains a challenge in gene regulatory research due to degeneracy and potential variability in binding sites in the genome. Dozens of algorithms designed to learn binding models (motifs) have generated many motifs available in research papers with a subset making it to databases like JASPAR, UniPROBE and Transfac. The presence of many versions of motifs from the various databases for a single TF and the lack of a standardized assessment technique makes it difficult for biologists to make an appropriate choice of binding model and for algorithm developers to benchmark, test and improve on their models. In this study, we review and evaluate the approaches in use, highlight differences and demonstrate the difficulty of defining a standardized motif assessment approach. We review scoring functions, motif length, test data and the type of performance metrics used in prior studies as some of the factors that influence the outcome of a motif assessment. We show that the scoring functions and statistics used in motif assessment influence ranking of motifs in a TF-specific manner. We also show that TF binding specificity can vary by source of genomic binding data. We also demonstrate that information content of a motif is not in isolation a measure of motif quality but is influenced by TF binding behaviour. We conclude that there is a need for an easy-to-use tool that presents all available evidence for a comparative analysis.
- Full Text:
- Authors: Kibet, Caleb K , Machanick, Philip
- Date: 2016
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/61169 , vital:27987 , http://dx.doi.org/10.12688/f1000research.7408.2
- Description: Transcription factor (TF) binding site prediction remains a challenge in gene regulatory research due to degeneracy and potential variability in binding sites in the genome. Dozens of algorithms designed to learn binding models (motifs) have generated many motifs available in research papers with a subset making it to databases like JASPAR, UniPROBE and Transfac. The presence of many versions of motifs from the various databases for a single TF and the lack of a standardized assessment technique makes it difficult for biologists to make an appropriate choice of binding model and for algorithm developers to benchmark, test and improve on their models. In this study, we review and evaluate the approaches in use, highlight differences and demonstrate the difficulty of defining a standardized motif assessment approach. We review scoring functions, motif length, test data and the type of performance metrics used in prior studies as some of the factors that influence the outcome of a motif assessment. We show that the scoring functions and statistics used in motif assessment influence ranking of motifs in a TF-specific manner. We also show that TF binding specificity can vary by source of genomic binding data. We also demonstrate that information content of a motif is not in isolation a measure of motif quality but is influenced by TF binding behaviour. We conclude that there is a need for an easy-to-use tool that presents all available evidence for a comparative analysis.
- Full Text:
Transforming the use of tutorials through academic staff development
- Clarence, Sherran, Wolff, Karin, Winberg, Simon, Farmer, Jean-Lee, Esambe, Emmanuel
- Authors: Clarence, Sherran , Wolff, Karin , Winberg, Simon , Farmer, Jean-Lee , Esambe, Emmanuel
- Date: 2016
- Language: English
- Type: text , conference publication
- Identifier: http://hdl.handle.net/10962/66982 , vital:29008
- Full Text:
- Authors: Clarence, Sherran , Wolff, Karin , Winberg, Simon , Farmer, Jean-Lee , Esambe, Emmanuel
- Date: 2016
- Language: English
- Type: text , conference publication
- Identifier: http://hdl.handle.net/10962/66982 , vital:29008
- Full Text:
Transitions into informal employment: an analysis of South African panel data: 2008-2012
- Authors: Muttze, Takudzwa
- Date: 2016
- Language: English
- Type: Thesis , Masters , MEcon
- Identifier: http://hdl.handle.net/10962/4498 , vital:20682
- Description: South Africa’s labour market is characterised by high unemployment but relatively low levels of informal employment, making it distinct from other developing countries. The existing literature appears to show evidence of high mobility rates of labour across labour market states. The coexistence of high labour mobility rates, yet high unemployment and weak informal employment in South Africa’s labour market is therefore puzzling. Considerable research has been done to explain this phenomenon and has suggested that barriers to informal entrepreneurship form the key reason why informal employment is relatively low in South Africa compared to other developing countries. Worker transitions have however not been a focal question in the literature. Using data from the National Tncome Dynamics Study (NTDS 2008-2012), this study sought to examine the characteristics of workers who move into informal employment, attaching importance to those who become self-employed. Transition matrices are constructed showing the proportion of workers who stayed or moved into different labour market states between 2008 and 2012, and linking the movements to 2008 personal characteristics. Churning between labour market states was found to be relatively high, albeit formal wage employment exhibiting immobility. Transitions out of informal employment were high, reflecting its survivalist nature. Conversely, those from unemployment into informal employment, particularly self-employment were low. Using the probit regression model, transitions to informal employment were found to be more associated with workers who are generally marginalised from formal employment opportunities. The results suggest that the South African labour market is to a larger extent not reflective of the Dualist narrative of ease of movement of workers from unemployment into informal employment and barriers into informal entrepreneurship are high. To date, policies which have sought to encourage informal entrepreneurship have not been a success. A central challenge to policymakers is to create an enabling environment for the unemployed to start their own informal businesses. This has the potential of reducing unemployment and poverty rates in the country.
- Full Text:
- Authors: Muttze, Takudzwa
- Date: 2016
- Language: English
- Type: Thesis , Masters , MEcon
- Identifier: http://hdl.handle.net/10962/4498 , vital:20682
- Description: South Africa’s labour market is characterised by high unemployment but relatively low levels of informal employment, making it distinct from other developing countries. The existing literature appears to show evidence of high mobility rates of labour across labour market states. The coexistence of high labour mobility rates, yet high unemployment and weak informal employment in South Africa’s labour market is therefore puzzling. Considerable research has been done to explain this phenomenon and has suggested that barriers to informal entrepreneurship form the key reason why informal employment is relatively low in South Africa compared to other developing countries. Worker transitions have however not been a focal question in the literature. Using data from the National Tncome Dynamics Study (NTDS 2008-2012), this study sought to examine the characteristics of workers who move into informal employment, attaching importance to those who become self-employed. Transition matrices are constructed showing the proportion of workers who stayed or moved into different labour market states between 2008 and 2012, and linking the movements to 2008 personal characteristics. Churning between labour market states was found to be relatively high, albeit formal wage employment exhibiting immobility. Transitions out of informal employment were high, reflecting its survivalist nature. Conversely, those from unemployment into informal employment, particularly self-employment were low. Using the probit regression model, transitions to informal employment were found to be more associated with workers who are generally marginalised from formal employment opportunities. The results suggest that the South African labour market is to a larger extent not reflective of the Dualist narrative of ease of movement of workers from unemployment into informal employment and barriers into informal entrepreneurship are high. To date, policies which have sought to encourage informal entrepreneurship have not been a success. A central challenge to policymakers is to create an enabling environment for the unemployed to start their own informal businesses. This has the potential of reducing unemployment and poverty rates in the country.
- Full Text:
Two in one: cryptic species discovered in biological control agent populations using molecular data and crossbreeding experiments
- Paterson, Iain D, Mangan, Rose, Downie, Douglas A, Coetzee, Julie A, Hill, Martin P, Burke, Ashley M, Downey, Paul O, Henry, Thomas J, Compton, Stephen G
- Authors: Paterson, Iain D , Mangan, Rose , Downie, Douglas A , Coetzee, Julie A , Hill, Martin P , Burke, Ashley M , Downey, Paul O , Henry, Thomas J , Compton, Stephen G
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/424877 , vital:72191 , xlink:href="https://doi.org/10.1002/ece3.2297"
- Description: There are many examples of cryptic species that have been identified through DNA-barcoding or other genetic techniques. There are, however, very few confirmations of cryptic species being reproductively isolated. This study presents one of the few cases of cryptic species that has been confirmed to be reproductively isolated and therefore true species according to the biological species concept. The cryptic species are of special interest because they were discovered within biological control agent populations. Two geographically isolated populations of Eccritotarsus catarinensis (Carvalho) [Hemiptera: Miridae], a biological control agent for the invasive aquatic macrophyte, water hyacinth, Eichhornia crassipes (Mart.) Solms [Pontederiaceae], in South Africa, were sampled from the native range of the species in South America. Morphological characteristics indicated that both populations were the same species according to the current taxonomy, but subsequent DNA analysis and breeding experiments revealed that the two populations are reproductively isolated. Crossbreeding experiments resulted in very few hybrid offspring when individuals were forced to interbreed with individuals of the other population, and no hybrid offspring were recorded when a choice of mate from either population was offered. The data indicate that the two populations are cryptic species that are reproductively incompatible. Subtle but reliable diagnostic characteristics were then identified to distinguish between the two species which would have been considered intraspecific variation without the data from the genetics and interbreeding experiments. These findings suggest that all consignments of biological control agents from allopatric populations should be screened for cryptic species using genetic techniques and that the importation of multiple consignments of the same species for biological control should be conducted with caution.
- Full Text:
- Authors: Paterson, Iain D , Mangan, Rose , Downie, Douglas A , Coetzee, Julie A , Hill, Martin P , Burke, Ashley M , Downey, Paul O , Henry, Thomas J , Compton, Stephen G
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/424877 , vital:72191 , xlink:href="https://doi.org/10.1002/ece3.2297"
- Description: There are many examples of cryptic species that have been identified through DNA-barcoding or other genetic techniques. There are, however, very few confirmations of cryptic species being reproductively isolated. This study presents one of the few cases of cryptic species that has been confirmed to be reproductively isolated and therefore true species according to the biological species concept. The cryptic species are of special interest because they were discovered within biological control agent populations. Two geographically isolated populations of Eccritotarsus catarinensis (Carvalho) [Hemiptera: Miridae], a biological control agent for the invasive aquatic macrophyte, water hyacinth, Eichhornia crassipes (Mart.) Solms [Pontederiaceae], in South Africa, were sampled from the native range of the species in South America. Morphological characteristics indicated that both populations were the same species according to the current taxonomy, but subsequent DNA analysis and breeding experiments revealed that the two populations are reproductively isolated. Crossbreeding experiments resulted in very few hybrid offspring when individuals were forced to interbreed with individuals of the other population, and no hybrid offspring were recorded when a choice of mate from either population was offered. The data indicate that the two populations are cryptic species that are reproductively incompatible. Subtle but reliable diagnostic characteristics were then identified to distinguish between the two species which would have been considered intraspecific variation without the data from the genetics and interbreeding experiments. These findings suggest that all consignments of biological control agents from allopatric populations should be screened for cryptic species using genetic techniques and that the importation of multiple consignments of the same species for biological control should be conducted with caution.
- Full Text:
Ulwaluko kwa Xhosa: young Xhosa men's lived experiences in the context of traditional male initiation
- Authors: Siswana, Anele
- Date: 2016
- Language: English
- Type: Thesis , Masters , MA
- Identifier: vital:3271 , http://hdl.handle.net/10962/d1020840
- Description: This thesis explores the lived experiences of young amaXhosa men in relation to U!walukokwa Xhosa (traditional male initiation [TMI]) and its impact on their sense of masculinity. The conceptual framework of this study is located within African epistemology focusing on indigenous knowledge systems (IKS) in South Africa. The study aimed at enabling young amaXhosa men who had undergone TMI to reflect on their first-hand, personal accounts of Ulwa/ukokwa Xhosa and manhood. Six semistructured interviews and a follow up focus group discussion were held with 23-27 years old amaXhosa men residing in Joza Township in Grahamstown, Eastern Cape. Participants were identified through purposive sampling. The thesis reports on the following findings: (a) the significance of the place/location of initiation, and the guise of modernity; (b) feelings of anticipation experienced by the young men; (c) the theme on ubudoda(manhood) affirmation Ndiyindoda!; (d) the theme on the concealment of pain (perseverance); (e) the theme on respect for self and others and ubuntu;(f) Uzimelegeqe (independence and autonomy) and (g) social role and responsibility. The paper argues for the relevance of TMI as a significantrite of passage from boyhood to manhood among amaXhosa men.
- Full Text:
- Authors: Siswana, Anele
- Date: 2016
- Language: English
- Type: Thesis , Masters , MA
- Identifier: vital:3271 , http://hdl.handle.net/10962/d1020840
- Description: This thesis explores the lived experiences of young amaXhosa men in relation to U!walukokwa Xhosa (traditional male initiation [TMI]) and its impact on their sense of masculinity. The conceptual framework of this study is located within African epistemology focusing on indigenous knowledge systems (IKS) in South Africa. The study aimed at enabling young amaXhosa men who had undergone TMI to reflect on their first-hand, personal accounts of Ulwa/ukokwa Xhosa and manhood. Six semistructured interviews and a follow up focus group discussion were held with 23-27 years old amaXhosa men residing in Joza Township in Grahamstown, Eastern Cape. Participants were identified through purposive sampling. The thesis reports on the following findings: (a) the significance of the place/location of initiation, and the guise of modernity; (b) feelings of anticipation experienced by the young men; (c) the theme on ubudoda(manhood) affirmation Ndiyindoda!; (d) the theme on the concealment of pain (perseverance); (e) the theme on respect for self and others and ubuntu;(f) Uzimelegeqe (independence and autonomy) and (g) social role and responsibility. The paper argues for the relevance of TMI as a significantrite of passage from boyhood to manhood among amaXhosa men.
- Full Text:
Un Langage, des Visions, une Passerelle:
- Authors: Tshilumba Mukendi, J S
- Date: 2016
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/146177 , vital:38502 , ISBN 9789074816496 , https://books.google.co.za/books?id=QDSdAQAACAAJanddq=Creer+en+postcolonie:+Voix+et+dissidences+belgo-congolaise+2010-2015andhl=enandsa=Xandved=0ahUKEwjts_Si_b_pAhXvShUIHWXwCd4Q6AEIJzAA
- Description: Book abstract. The authors and artists (Baloji, Toma Muteba Luntumbue, Nganji Laeh, Nina Miskina, Joëlle Sambi, Sarah Arens, Heleen Debeuckelaere, Bénédicte Kumbi ...) who contributed to the work to debate the Belgian postcolonial question and it will be punctuated by poetic and musical stops.
- Full Text:
- Authors: Tshilumba Mukendi, J S
- Date: 2016
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/146177 , vital:38502 , ISBN 9789074816496 , https://books.google.co.za/books?id=QDSdAQAACAAJanddq=Creer+en+postcolonie:+Voix+et+dissidences+belgo-congolaise+2010-2015andhl=enandsa=Xandved=0ahUKEwjts_Si_b_pAhXvShUIHWXwCd4Q6AEIJzAA
- Description: Book abstract. The authors and artists (Baloji, Toma Muteba Luntumbue, Nganji Laeh, Nina Miskina, Joëlle Sambi, Sarah Arens, Heleen Debeuckelaere, Bénédicte Kumbi ...) who contributed to the work to debate the Belgian postcolonial question and it will be punctuated by poetic and musical stops.
- Full Text:
Understanding how grade 8 Physical Science teachers make use of learners’ prior everyday knowledge when teaching static electricity: A case study
- Authors: Iyambo, Toini
- Date: 2016
- Language: English
- Type: Thesis , Masters , MEd
- Identifier: http://hdl.handle.net/10962/1320 , vital:20046
- Description: Over the last decade of my teaching I have been grappling with how to incorporate learners’ prior everyday knowledge into my Physical Science lessons to enable me to close the gap between school science and everyday knowledge. I conducted this case study in two schools, one in Omusati region and one in Ohangwena Region, Namibia. Its purpose was to investigate how grade 8 Physical Science teachers make use of learners’ prior everyday knowledge when teaching the topic of static electricity. Underpinned by an interpretive paradigm, the study made use of document analysis, observation (lessons were also video-taped) and semi-structured interviews to generate the data. Three data generating techniques were used for triangulation and validation purposes. To further validate the data, transcripts of video-taped lessons and interviews were sent back to the research participants for member checking. The main findings of my study are that teachers did incorporate learners’ prior knowledge in the lesson presentation on static electricity. It emerged from the study that, learners possess a great deal of prior everyday scientific and non-scientific knowledge and experiences about static electricity that they had acquired from their communities. Also, mobilization of learners' everyday knowledge and experiences about static electricity enabled learner engagement during the science lessons. Likewise, engaging learners in demonstrations on static electricity helped them to make meaning of the scientific concepts involved in the topic. It also emerged from this study that teachers face challenges of lack of documentation of indigenous knowledge which is potentially a form of prior knowledge, language barriers and a lack of resources. Based on my research findings, I therefore, recommend that learners' prior everyday knowledge and experiences about static electricity should be incorporated during the teaching and learning process.
- Full Text:
- Authors: Iyambo, Toini
- Date: 2016
- Language: English
- Type: Thesis , Masters , MEd
- Identifier: http://hdl.handle.net/10962/1320 , vital:20046
- Description: Over the last decade of my teaching I have been grappling with how to incorporate learners’ prior everyday knowledge into my Physical Science lessons to enable me to close the gap between school science and everyday knowledge. I conducted this case study in two schools, one in Omusati region and one in Ohangwena Region, Namibia. Its purpose was to investigate how grade 8 Physical Science teachers make use of learners’ prior everyday knowledge when teaching the topic of static electricity. Underpinned by an interpretive paradigm, the study made use of document analysis, observation (lessons were also video-taped) and semi-structured interviews to generate the data. Three data generating techniques were used for triangulation and validation purposes. To further validate the data, transcripts of video-taped lessons and interviews were sent back to the research participants for member checking. The main findings of my study are that teachers did incorporate learners’ prior knowledge in the lesson presentation on static electricity. It emerged from the study that, learners possess a great deal of prior everyday scientific and non-scientific knowledge and experiences about static electricity that they had acquired from their communities. Also, mobilization of learners' everyday knowledge and experiences about static electricity enabled learner engagement during the science lessons. Likewise, engaging learners in demonstrations on static electricity helped them to make meaning of the scientific concepts involved in the topic. It also emerged from this study that teachers face challenges of lack of documentation of indigenous knowledge which is potentially a form of prior knowledge, language barriers and a lack of resources. Based on my research findings, I therefore, recommend that learners' prior everyday knowledge and experiences about static electricity should be incorporated during the teaching and learning process.
- Full Text:
Understanding how the incorporation of indigenous knowledge (IK) enables or constrains the teaching and learning of alcoholic fermentation in Life Sciences in Grade 11
- Authors: Mutanho, Chrispen
- Date: 2016
- Language: English
- Type: Thesis , Masters , MEd
- Identifier: http://hdl.handle.net/10962/1264 , vital:20041
- Description: There is growing interest in the role of indigenous knowledge (IK) in science education in many parts of the world. In South Africa, this comes against the backdrop of a long history of cultural alienation, neglect and suppression of the IK of the indigenous people by colonial governments. Hence, the first post-independence National Curriculum Policy Statement (Curriculum, 2005) and its subsequent modified versions emphasised the need to redress the imbalances of the past so as to make science accessible to learners from diverse cultural backgrounds. However, literature reveals that the efforts to implement an IK-based curriculum are constrained by the lack of clarity, knowledge and skills on how to effectively make use of IK in the classroom situation so as to bring about effective teaching and learning. Against this background, this study sought to understand how the incorporation of IK enables or constrains the teaching and learning of alcoholic fermentation. Underpinned by an interpretive paradigm, a qualitative case study was conducted at a high school in Mthatha District in the Eastern Cape Province of South Africa. The study comprised of a sample of ten Life Sciences teachers from four neighbouring high schools, two Grade 11 Life Sciences teachers and their classes and two focus groups of six learners from each class. Convenience and purposive sampling were used to select the participants and the research site. The study made use of a questionnaire, document analysis, lesson observation, stimulated recall interviews and focus group interviews to generate data. The questionnaire sought to get an overview of Life Sciences teachers’ attitudes, opinions and experiences on incorporating IK in science teaching. The data gathered were then used as baseline information to inform the main study. The lesson observations, stimulated recall interviews and the focus group interviews sought to understand how the incorporation of IK enables or constrains the teaching and learning of alcoholic fermentation. Document analysis, lesson observation, stimulated recall interviews and focus group interviews were conducted to understand the experience of incorporating IK in a real life classroom situation. The study was informed by Vygotsky’s socio-cultural constructivism and Shulman’s pedagogical content knowledge (PCK) theory. From Vygotsky’s theory I borrowed the idea of mediated learning, scaffolding (Bruner, 1986), zone of proximal development (ZPD), as well as the use of language and cultural artefacts as tools of analysis of the classroom interaction between the teacher and the learners during the teaching-learning process. Shulman’s theory of PCK was also used to analyse how teachers apply IK in teaching Science. The data obtained were coded inductively and presented in tables, graphs and thick descriptive texts to make it easy to understand. The findings of this research show that incorporating IK improved the teaching-learning process by arousing learners’ interest in science, increasing learners’ participation and motivation, meaning making, language use, questioning and engagement in the learning process. Teaching became learner-centred, for it was directed by learners’ questions. Collaborative learning through group discussions, debates, arguments and brainstorming emerged to be an effective way of engaging learners in learning. The teachers used probing to encourage critical thinking before scaffolding learners. However, even though teachers generally accept IK as valuable in their teaching they lack the pedagogical content knowledge to effectively incorporate it into meaningful teaching and learning. Furthermore, teachers viewed cultural diversity as a constraint to their efforts to incorporate IK in teaching science. On the contrary, their learners held the view that having cultural diversity in classrooms created an opportunity to learn from other people’s cultures. Variables such as experience and difference in the cultural background of learners and teachers alike, tended to affect the teachers’ ability to incorporate IK.
- Full Text:
- Authors: Mutanho, Chrispen
- Date: 2016
- Language: English
- Type: Thesis , Masters , MEd
- Identifier: http://hdl.handle.net/10962/1264 , vital:20041
- Description: There is growing interest in the role of indigenous knowledge (IK) in science education in many parts of the world. In South Africa, this comes against the backdrop of a long history of cultural alienation, neglect and suppression of the IK of the indigenous people by colonial governments. Hence, the first post-independence National Curriculum Policy Statement (Curriculum, 2005) and its subsequent modified versions emphasised the need to redress the imbalances of the past so as to make science accessible to learners from diverse cultural backgrounds. However, literature reveals that the efforts to implement an IK-based curriculum are constrained by the lack of clarity, knowledge and skills on how to effectively make use of IK in the classroom situation so as to bring about effective teaching and learning. Against this background, this study sought to understand how the incorporation of IK enables or constrains the teaching and learning of alcoholic fermentation. Underpinned by an interpretive paradigm, a qualitative case study was conducted at a high school in Mthatha District in the Eastern Cape Province of South Africa. The study comprised of a sample of ten Life Sciences teachers from four neighbouring high schools, two Grade 11 Life Sciences teachers and their classes and two focus groups of six learners from each class. Convenience and purposive sampling were used to select the participants and the research site. The study made use of a questionnaire, document analysis, lesson observation, stimulated recall interviews and focus group interviews to generate data. The questionnaire sought to get an overview of Life Sciences teachers’ attitudes, opinions and experiences on incorporating IK in science teaching. The data gathered were then used as baseline information to inform the main study. The lesson observations, stimulated recall interviews and the focus group interviews sought to understand how the incorporation of IK enables or constrains the teaching and learning of alcoholic fermentation. Document analysis, lesson observation, stimulated recall interviews and focus group interviews were conducted to understand the experience of incorporating IK in a real life classroom situation. The study was informed by Vygotsky’s socio-cultural constructivism and Shulman’s pedagogical content knowledge (PCK) theory. From Vygotsky’s theory I borrowed the idea of mediated learning, scaffolding (Bruner, 1986), zone of proximal development (ZPD), as well as the use of language and cultural artefacts as tools of analysis of the classroom interaction between the teacher and the learners during the teaching-learning process. Shulman’s theory of PCK was also used to analyse how teachers apply IK in teaching Science. The data obtained were coded inductively and presented in tables, graphs and thick descriptive texts to make it easy to understand. The findings of this research show that incorporating IK improved the teaching-learning process by arousing learners’ interest in science, increasing learners’ participation and motivation, meaning making, language use, questioning and engagement in the learning process. Teaching became learner-centred, for it was directed by learners’ questions. Collaborative learning through group discussions, debates, arguments and brainstorming emerged to be an effective way of engaging learners in learning. The teachers used probing to encourage critical thinking before scaffolding learners. However, even though teachers generally accept IK as valuable in their teaching they lack the pedagogical content knowledge to effectively incorporate it into meaningful teaching and learning. Furthermore, teachers viewed cultural diversity as a constraint to their efforts to incorporate IK in teaching science. On the contrary, their learners held the view that having cultural diversity in classrooms created an opportunity to learn from other people’s cultures. Variables such as experience and difference in the cultural background of learners and teachers alike, tended to affect the teachers’ ability to incorporate IK.
- Full Text:
Understanding sexual concurrency and HIV/AIDS: implicit and explicit attitudes in a South African student population
- Authors: Malataliana, Maleeto Lucy
- Date: 2016
- Language: English
- Type: Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/3335 , vital:20484
- Description: There are more people infected with HIV in South Africa, than in any other country in the world. Studies indicate a plausible relationship between concurrently organised sexual partnership and the spread of STIs, with concurrency being accountable for as much as 74% of HIV infections in South Africa. Understanding sexual concurrency is therefore of vital importance, especially in the South African perspective. It has, however, become increasingly unreliable to rely solely on explicit self-measures to study sexual concurrency, and research has suggested that implicit cognition is a reliable alternative to understanding sexual behaviour and attitudes towards sexuality, which cannot be directly measured by explicit means. The purpose of this study was to understand sexual concurrency among a population of university students by researching their implicit and explicit attitudes towards sexual concurrency; and thereby to aid in understanding sexual concurrency in relation to the spread of HIV. A quantitative research methodology was used to analyse results from explicit measures of sexual concurrency in the form of a questionnaire, and implicit measures of sexual concurrency in the form of the Implicit Association Test (IAT). Although no correlation existed between implicit and explicit measures attitudes towards sexual concurrency, it was, however, observed that sexual concurrency has and is being broadly practiced, and that age is a key determinant for sexual concurrency.
- Full Text:
- Authors: Malataliana, Maleeto Lucy
- Date: 2016
- Language: English
- Type: Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/3335 , vital:20484
- Description: There are more people infected with HIV in South Africa, than in any other country in the world. Studies indicate a plausible relationship between concurrently organised sexual partnership and the spread of STIs, with concurrency being accountable for as much as 74% of HIV infections in South Africa. Understanding sexual concurrency is therefore of vital importance, especially in the South African perspective. It has, however, become increasingly unreliable to rely solely on explicit self-measures to study sexual concurrency, and research has suggested that implicit cognition is a reliable alternative to understanding sexual behaviour and attitudes towards sexuality, which cannot be directly measured by explicit means. The purpose of this study was to understand sexual concurrency among a population of university students by researching their implicit and explicit attitudes towards sexual concurrency; and thereby to aid in understanding sexual concurrency in relation to the spread of HIV. A quantitative research methodology was used to analyse results from explicit measures of sexual concurrency in the form of a questionnaire, and implicit measures of sexual concurrency in the form of the Implicit Association Test (IAT). Although no correlation existed between implicit and explicit measures attitudes towards sexual concurrency, it was, however, observed that sexual concurrency has and is being broadly practiced, and that age is a key determinant for sexual concurrency.
- Full Text:
Unpacking Pandora’s box: Understanding and categorising ecosystem disservices for environmental management and human wellbeing
- Shackleton, Charlie M, Ruwanza, Sheunesu, Sinasson Sanni, Gisele, Bennett, S, De Lacy, Peter, Modipa, Rebone D, Mtati, Nosiseko, Sachikonye, Mwazvita T B, Thondhlana, Gladman
- Authors: Shackleton, Charlie M , Ruwanza, Sheunesu , Sinasson Sanni, Gisele , Bennett, S , De Lacy, Peter , Modipa, Rebone D , Mtati, Nosiseko , Sachikonye, Mwazvita T B , Thondhlana, Gladman
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/182113 , vital:43801 , xlink:href="https://doi.org/10.1007/s10021-015-9952-z"
- Description: Research into the benefits that ecosystems contribute to human wellbeing has multiplied over the last few years following from the seminal contributions of the international Millennium Ecosystem Assessment. In comparison, the fact that some ecosystem goods and services undermine or harm human wellbeing has been seriously overlooked. These negative impacts have become known as ecosystem disservices. The neglect of ecosystem disservices is problematic because investments into the management or reduction of ecosystem disservices may yield better outcomes for human wellbeing, or at a lower investment, than management of ecosystem services. Additionally, management to optimise specific ecosystem services may simultaneously exacerbate associated disservices. We posit that one reason for the neglect of ecosystem disservices from the discourse and policy debates around ecosystems and human wellbeing is because there is no widely accepted definition or typology of ecosystem disservices. Here, we briefly examine current understandings of the term ecosystem disservices and offer a definition and a working typology to help generate debate, policy and management options around ecosystem disservices. We differentiate ecosystem disservices from natural hazards and social hazards, consider some of their inherent properties and then classify them into six categories. A variety of examples are used to illustrate the different types of, and management strategies to, ecosystem disservices.
- Full Text:
- Authors: Shackleton, Charlie M , Ruwanza, Sheunesu , Sinasson Sanni, Gisele , Bennett, S , De Lacy, Peter , Modipa, Rebone D , Mtati, Nosiseko , Sachikonye, Mwazvita T B , Thondhlana, Gladman
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/182113 , vital:43801 , xlink:href="https://doi.org/10.1007/s10021-015-9952-z"
- Description: Research into the benefits that ecosystems contribute to human wellbeing has multiplied over the last few years following from the seminal contributions of the international Millennium Ecosystem Assessment. In comparison, the fact that some ecosystem goods and services undermine or harm human wellbeing has been seriously overlooked. These negative impacts have become known as ecosystem disservices. The neglect of ecosystem disservices is problematic because investments into the management or reduction of ecosystem disservices may yield better outcomes for human wellbeing, or at a lower investment, than management of ecosystem services. Additionally, management to optimise specific ecosystem services may simultaneously exacerbate associated disservices. We posit that one reason for the neglect of ecosystem disservices from the discourse and policy debates around ecosystems and human wellbeing is because there is no widely accepted definition or typology of ecosystem disservices. Here, we briefly examine current understandings of the term ecosystem disservices and offer a definition and a working typology to help generate debate, policy and management options around ecosystem disservices. We differentiate ecosystem disservices from natural hazards and social hazards, consider some of their inherent properties and then classify them into six categories. A variety of examples are used to illustrate the different types of, and management strategies to, ecosystem disservices.
- Full Text:
User interface design guidelines for digital television virtual remote controls
- Authors: Wentzel, Alicia Veronica
- Date: 2016
- Subjects: Remote control , User interfaces (Computer systems) , Television broadcasting , Human-computer interaction
- Language: English
- Type: Thesis , Masters , MCom
- Identifier: vital:1158 , http://hdl.handle.net/10962/d1020617
- Description: The remote control is a pivotal component in households worldwide. It helps users enjoy leisurely television (TV) viewing. The remote control has various user interfaces that people interact with. For example, the physical user interface includes the shape of the remote and the physical buttons; the logical user interface refers to how the information is laid out; and the graphical user interface refers to the colours and aesthetic features of the remote control. All of the user interfaces together with the context of use, cultural factors, social factors, and prior experiences of the user influences the ways people interact with their remote control and ultimately has an effect on their user experiences. Advances in the broadcasting sector and transformations of the TV physical remote control have compounded the simple remote control into a multifaceted, indispensable device, overcrowded with buttons. The usability and ultimately the user experience of physical remote controls (PRCs) have been affected by the overloaded functionality and small button sizes. The usability issues with current PRCs, the evolution of mobile phones into touchscreen smartphones, and the trend of global companies moving towards virtual remote controls (VRCs) have prompted this research to discover what user interface design features will contribute towards an enhanced user experience for digital TV VRCs. This research used the design science research process model (DSRP), which comprised six steps, to investigate this topic area further. A review of the domain literature pertaining to mobile user experiences (MUX) and all the encompassing factors, mobile human computer interaction (MHCI) and the physical, logical, graphical and natural user interfaces was completed, as well as a review of the literature regarding the usability issues of PRCs and VRCs. A contextual task analysis (CTA) of a single South African digital TV PRC was used to identify how users utilise PRCs to perform tasks, and the usability issues they encountered during the tasks. Brainstorming focus groups were used to understand how to represent certain user interface elements and attempted to source ideas from users about what potential functionality digital TV VRCs should contain. Together with all the other results gathered from the previous chapters amalgamated into a set of user interface design guidelines for digital TV VRCs. The proposed user interface guidelines were used to instantiate a digital TV VRC prototype that underwent usability testing in order to validate the proposed user interface design guidelines. The results of the usability testing revealed that the user interface design guidelines for digital TV VRCs were successful, with the addition of one guideline that was discovered during the usability testing.
- Full Text:
- Authors: Wentzel, Alicia Veronica
- Date: 2016
- Subjects: Remote control , User interfaces (Computer systems) , Television broadcasting , Human-computer interaction
- Language: English
- Type: Thesis , Masters , MCom
- Identifier: vital:1158 , http://hdl.handle.net/10962/d1020617
- Description: The remote control is a pivotal component in households worldwide. It helps users enjoy leisurely television (TV) viewing. The remote control has various user interfaces that people interact with. For example, the physical user interface includes the shape of the remote and the physical buttons; the logical user interface refers to how the information is laid out; and the graphical user interface refers to the colours and aesthetic features of the remote control. All of the user interfaces together with the context of use, cultural factors, social factors, and prior experiences of the user influences the ways people interact with their remote control and ultimately has an effect on their user experiences. Advances in the broadcasting sector and transformations of the TV physical remote control have compounded the simple remote control into a multifaceted, indispensable device, overcrowded with buttons. The usability and ultimately the user experience of physical remote controls (PRCs) have been affected by the overloaded functionality and small button sizes. The usability issues with current PRCs, the evolution of mobile phones into touchscreen smartphones, and the trend of global companies moving towards virtual remote controls (VRCs) have prompted this research to discover what user interface design features will contribute towards an enhanced user experience for digital TV VRCs. This research used the design science research process model (DSRP), which comprised six steps, to investigate this topic area further. A review of the domain literature pertaining to mobile user experiences (MUX) and all the encompassing factors, mobile human computer interaction (MHCI) and the physical, logical, graphical and natural user interfaces was completed, as well as a review of the literature regarding the usability issues of PRCs and VRCs. A contextual task analysis (CTA) of a single South African digital TV PRC was used to identify how users utilise PRCs to perform tasks, and the usability issues they encountered during the tasks. Brainstorming focus groups were used to understand how to represent certain user interface elements and attempted to source ideas from users about what potential functionality digital TV VRCs should contain. Together with all the other results gathered from the previous chapters amalgamated into a set of user interface design guidelines for digital TV VRCs. The proposed user interface guidelines were used to instantiate a digital TV VRC prototype that underwent usability testing in order to validate the proposed user interface design guidelines. The results of the usability testing revealed that the user interface design guidelines for digital TV VRCs were successful, with the addition of one guideline that was discovered during the usability testing.
- Full Text:
Using bioinformatics tools to screen for trypanosomal cathepsin B cysteine protease inhibitors from the SANCDB as a novel therapeutic modality against Human African Trypanosomiasis (HAT)
- Authors: Mokhawa, Gaone
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3304 , vital:20470
- Description: Human African Trypanosomiasis (HAT), also known as sleeping sickness, is a fatal chronic disease that is caused by flagellated protozoans, Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense. HAT is spread by a bite from an infected tsetse fly of the Glosina genus. Up to 60 million people in 36 countries in sub-Saharan Africa are at a risk of infection from HAT with up to 30 000 deaths reported every year. Current chemotherapy for HAT is insufficient since the available drugs exhibit unacceptable side effects (toxicity) and parasite resistance. Novel treatments and approaches for development of specific and more potent drugs for HAT are therefore required. One approach is to target vital proteins that are essential to the life cycle of the parasite. The main interest of this study is to explore Trypanosoma brucei cathepsin B-like protease (TbCatB) structural and functional properties with the primary goal of discovering non peptide small molecule inhibitors of TbCatB using bioinformatics approaches. TbCatB is a papain family C1 cysteine protease which belongs to clan CA group and it has emerged as a potential HAT drug target. Papain family cysteine proteases of Clan CA group of Trypanosoma brucei (rhodesain and TbCatB) have demonstrated potential as chemotherapeutic targets using synthetic protease inhibitors like Z-Phe-Ala-CHN2 to kill the parasite in vitro and in vivo. TbCatB has been identified as the essential cysteine protease of T. brucei since mRNA silencing of TbCatB killed the parasite and resulted in a cure in mice infected with T. brucei while mRNA silencing of rhodesain only extended mice life. TbCatB is therefore a promising drug target against HAT and the discovery and development of compounds that can selectively inhibit TbCatB without posing any danger to the human host represent a great therapeutic solution for treatment of HAT. To understand protein-inhibitor interactions, useful information can be obtained from high resolution protease-inhibitor crystal structure complexes. This study aims to use bioinformatics approaches to carry out comparative sequence, structural and functional analysis of TbCatB protease and its homologs from T. congolense, T, cruzi, T. vivax and H. sapien as well as to identify non-peptide small molecule inhibitors of TbCatB cysteine proteases from natural compounds of South African origin. Sequences of TbCatB (PDB ID: 3HHI) homologs were retrieved by a BLAST search. Human cathepsin B (PDB ID: 3CBJ) was selected from a list of templates for homology modelling found by HHpred. MODELLER version 9.10 program was used to generate a hundred models for T. congolense, T, cruzi and T. vivax cathepsin B like proteases using 3HHI and 3CBJ as templates. The best models were chosen based on their low DOPE Z scores before validation using MetaMQAPII, ANOLEA, PROCHECK and QMEAN6. The DOPE Z scores and the RMSD (RMS) values of the calculated models indicate that the models are of acceptable energy (stability) and fold (conformation). Results from the different MQAPs indicate the models are of acceptable quality and they can be used for docking studies. High throughput screening of SANCDB using AutoDock Vina revealed nine compounds, SANC00 478, 479, 480, 481, 482, 488, 489, 490 and 491, having a strong affinity for Trypanosoma spp. cathepsin B proteases than HsCatB. SANC00488 has the strongest binding to Trypanosoma spp. cathepsin B proteases and the weakest binding to HsCatB protease. Molecular dynamics (MD) simulations show that the complexes between SANC00488 and TbCatB, TcCatB, TcrCatB and TvCatB are stable and do not come apart during simulation. The complex between this compound and HsCatB however is unstable and comes apart during simulation. Residues that are important for the stability of SANC00488-TbCatB complex are Gly328 of the S2 subsite, Phe208, and Ala256. In conclusion SANC00488 is a good candidate for development of a drug against HAT.
- Full Text:
- Authors: Mokhawa, Gaone
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3304 , vital:20470
- Description: Human African Trypanosomiasis (HAT), also known as sleeping sickness, is a fatal chronic disease that is caused by flagellated protozoans, Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense. HAT is spread by a bite from an infected tsetse fly of the Glosina genus. Up to 60 million people in 36 countries in sub-Saharan Africa are at a risk of infection from HAT with up to 30 000 deaths reported every year. Current chemotherapy for HAT is insufficient since the available drugs exhibit unacceptable side effects (toxicity) and parasite resistance. Novel treatments and approaches for development of specific and more potent drugs for HAT are therefore required. One approach is to target vital proteins that are essential to the life cycle of the parasite. The main interest of this study is to explore Trypanosoma brucei cathepsin B-like protease (TbCatB) structural and functional properties with the primary goal of discovering non peptide small molecule inhibitors of TbCatB using bioinformatics approaches. TbCatB is a papain family C1 cysteine protease which belongs to clan CA group and it has emerged as a potential HAT drug target. Papain family cysteine proteases of Clan CA group of Trypanosoma brucei (rhodesain and TbCatB) have demonstrated potential as chemotherapeutic targets using synthetic protease inhibitors like Z-Phe-Ala-CHN2 to kill the parasite in vitro and in vivo. TbCatB has been identified as the essential cysteine protease of T. brucei since mRNA silencing of TbCatB killed the parasite and resulted in a cure in mice infected with T. brucei while mRNA silencing of rhodesain only extended mice life. TbCatB is therefore a promising drug target against HAT and the discovery and development of compounds that can selectively inhibit TbCatB without posing any danger to the human host represent a great therapeutic solution for treatment of HAT. To understand protein-inhibitor interactions, useful information can be obtained from high resolution protease-inhibitor crystal structure complexes. This study aims to use bioinformatics approaches to carry out comparative sequence, structural and functional analysis of TbCatB protease and its homologs from T. congolense, T, cruzi, T. vivax and H. sapien as well as to identify non-peptide small molecule inhibitors of TbCatB cysteine proteases from natural compounds of South African origin. Sequences of TbCatB (PDB ID: 3HHI) homologs were retrieved by a BLAST search. Human cathepsin B (PDB ID: 3CBJ) was selected from a list of templates for homology modelling found by HHpred. MODELLER version 9.10 program was used to generate a hundred models for T. congolense, T, cruzi and T. vivax cathepsin B like proteases using 3HHI and 3CBJ as templates. The best models were chosen based on their low DOPE Z scores before validation using MetaMQAPII, ANOLEA, PROCHECK and QMEAN6. The DOPE Z scores and the RMSD (RMS) values of the calculated models indicate that the models are of acceptable energy (stability) and fold (conformation). Results from the different MQAPs indicate the models are of acceptable quality and they can be used for docking studies. High throughput screening of SANCDB using AutoDock Vina revealed nine compounds, SANC00 478, 479, 480, 481, 482, 488, 489, 490 and 491, having a strong affinity for Trypanosoma spp. cathepsin B proteases than HsCatB. SANC00488 has the strongest binding to Trypanosoma spp. cathepsin B proteases and the weakest binding to HsCatB protease. Molecular dynamics (MD) simulations show that the complexes between SANC00488 and TbCatB, TcCatB, TcrCatB and TvCatB are stable and do not come apart during simulation. The complex between this compound and HsCatB however is unstable and comes apart during simulation. Residues that are important for the stability of SANC00488-TbCatB complex are Gly328 of the S2 subsite, Phe208, and Ala256. In conclusion SANC00488 is a good candidate for development of a drug against HAT.
- Full Text:
Views from the inside: An appraisal of the effectiveness of international NGOs as agents of development through a case study of Concern Universal’s Local Development Support Programme in Dedza District, Malawi
- Authors: Mussa, Khadija Sungeni
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSocSc
- Identifier: http://hdl.handle.net/10962/1499 , vital:20063
- Description: Malawi, which became independent in 1964, attracted Non-Governmental Organisations (NGOs) from the early 1980s. Initially, NGO involvement was a response to the influx of refugees from neighbouring war-torn Mozambique. Since then, NGOs have been active in the development sector. Malawi, a small country, has widespread poverty, and has recently been in international headlines as a victim of floods, drought and food shortages. Economically unstable, with environmental problems, Malawi is in need of development assistance. NGOs have been centrally positioned in such efforts, but the academic literature on their role has been limited. NGO interventions in development efforts, generally, have been subject to controversy. While some argue that NGOs provide an essential means of development, especially where state capacity is limited, others argue that, with most NGOs headquartered or funded from abroad, their strategies and practices are often more accountable to external pressures than local needs. This thesis intervenes in these debates with a case study: with the aim of examining the sustainability, appropriateness, accountability and effectiveness of NGO projects, it looks at a project by the international NGO (INGO), Concern Universal (CU), which works in the central region in Dedza, Malawi. It examines the project, using fieldwork in three villages, looking at issues such as its use of participatory methods, relations with local government and village structures, capacity building methods, and donor relations. The thesis argues that (I)NGOs like CU exist in a conflicted situation: they have to remain in the good books of their donors, while, at the same time, maintaining accountability to their beneficiaries; they depend on their ability to manoeuvre through the conflict in order to ensure their continuity, and so, their impact is shaped by competing imperatives. CU has made a real impact on poverty alleviation efforts, but its methods and approaches are shaped by said competing imperatives.
- Full Text:
- Authors: Mussa, Khadija Sungeni
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSocSc
- Identifier: http://hdl.handle.net/10962/1499 , vital:20063
- Description: Malawi, which became independent in 1964, attracted Non-Governmental Organisations (NGOs) from the early 1980s. Initially, NGO involvement was a response to the influx of refugees from neighbouring war-torn Mozambique. Since then, NGOs have been active in the development sector. Malawi, a small country, has widespread poverty, and has recently been in international headlines as a victim of floods, drought and food shortages. Economically unstable, with environmental problems, Malawi is in need of development assistance. NGOs have been centrally positioned in such efforts, but the academic literature on their role has been limited. NGO interventions in development efforts, generally, have been subject to controversy. While some argue that NGOs provide an essential means of development, especially where state capacity is limited, others argue that, with most NGOs headquartered or funded from abroad, their strategies and practices are often more accountable to external pressures than local needs. This thesis intervenes in these debates with a case study: with the aim of examining the sustainability, appropriateness, accountability and effectiveness of NGO projects, it looks at a project by the international NGO (INGO), Concern Universal (CU), which works in the central region in Dedza, Malawi. It examines the project, using fieldwork in three villages, looking at issues such as its use of participatory methods, relations with local government and village structures, capacity building methods, and donor relations. The thesis argues that (I)NGOs like CU exist in a conflicted situation: they have to remain in the good books of their donors, while, at the same time, maintaining accountability to their beneficiaries; they depend on their ability to manoeuvre through the conflict in order to ensure their continuity, and so, their impact is shaped by competing imperatives. CU has made a real impact on poverty alleviation efforts, but its methods and approaches are shaped by said competing imperatives.
- Full Text:
Visit the exotic birthplaces of transdisciplinarity
- Burt, Jane C, Cockburn, Jessica J, Fox, Helen E, Copteros, Athina
- Authors: Burt, Jane C , Cockburn, Jessica J , Fox, Helen E , Copteros, Athina
- Date: 2016
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/68442 , vital:29256 , https://doi.org/10.13140/RG.2.1.1511.7048
- Description: Publisher version , Preface: Why a new approach to science? The world we live in is very different to the world of one hundred years ago. The world has never been so populated by humans and never before have the spe-cies ‘human’ influenced and manipulated the natural world in the way in which we do now. Academics are calling it the age of the Anthropocene. In the age of the Anthropocene we face different challenges to what hu- mans faced centuries ago. As we find ourselves in this new age we have had to not only question ‘what we know’ but also ‘how we know’ and whether the ‘how we know’ is the right kind of ‘how’ for the problems that we face today. This has led to a questioning of the way in which we generate knowledge and the way in which this knowledge is used. This critique is not aimed at all knowledge generation it is mostly a frustration that has arisen out of the physical and biological sciences with the realisation that doing good science is just not enough to bring about meaningful change in the world. Trans-disciplinary scientists and practitioners have begun this journey in search of a new kind of science - A science in service of society! This tourist trip will re- trace the few first steps of these emerging ideas so that we can understand where these new ideas have come from and how they may influence our own research. , This document was developed for a postgraduate course on Transdisciplinary research held at Rhodes University. It explores three key theoretical approaches to transdisciplinarity in relation to the question 'Why TD?'.
- Full Text:
- Authors: Burt, Jane C , Cockburn, Jessica J , Fox, Helen E , Copteros, Athina
- Date: 2016
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/68442 , vital:29256 , https://doi.org/10.13140/RG.2.1.1511.7048
- Description: Publisher version , Preface: Why a new approach to science? The world we live in is very different to the world of one hundred years ago. The world has never been so populated by humans and never before have the spe-cies ‘human’ influenced and manipulated the natural world in the way in which we do now. Academics are calling it the age of the Anthropocene. In the age of the Anthropocene we face different challenges to what hu- mans faced centuries ago. As we find ourselves in this new age we have had to not only question ‘what we know’ but also ‘how we know’ and whether the ‘how we know’ is the right kind of ‘how’ for the problems that we face today. This has led to a questioning of the way in which we generate knowledge and the way in which this knowledge is used. This critique is not aimed at all knowledge generation it is mostly a frustration that has arisen out of the physical and biological sciences with the realisation that doing good science is just not enough to bring about meaningful change in the world. Trans-disciplinary scientists and practitioners have begun this journey in search of a new kind of science - A science in service of society! This tourist trip will re- trace the few first steps of these emerging ideas so that we can understand where these new ideas have come from and how they may influence our own research. , This document was developed for a postgraduate course on Transdisciplinary research held at Rhodes University. It explores three key theoretical approaches to transdisciplinarity in relation to the question 'Why TD?'.
- Full Text:
Walking into Africa in a Chinese way: Hua Jiming’s mindful entry as counterbalance
- Authors: Simbao, Ruth K
- Date: 2016
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/146167 , vital:38501 , ISBN 9791024005799 , https://books.google.co.za/books?id=VGSwDwAAQBAJanddq=Afrique-Asie:+Arts,+espaces,+pratiquesandsource=gbs_navlinks_s
- Description: Book abstract. The links between Africa and Asia are at the very heart of globalization. Understanding its richness and complexity requires a study carried out from various points of view. Particular attention to culture is essential. Centered on the work of visual artists and performers, on town planning, literature and spirituality, the essays gathered here call on many disciplines: art history and history, anthropology, sociology, geography, architecture, comparative literature, visual and culture studies. They constitute a network of crossed views on a subject which no serious reflection on globalization can do today.
- Full Text:
- Authors: Simbao, Ruth K
- Date: 2016
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/146167 , vital:38501 , ISBN 9791024005799 , https://books.google.co.za/books?id=VGSwDwAAQBAJanddq=Afrique-Asie:+Arts,+espaces,+pratiquesandsource=gbs_navlinks_s
- Description: Book abstract. The links between Africa and Asia are at the very heart of globalization. Understanding its richness and complexity requires a study carried out from various points of view. Particular attention to culture is essential. Centered on the work of visual artists and performers, on town planning, literature and spirituality, the essays gathered here call on many disciplines: art history and history, anthropology, sociology, geography, architecture, comparative literature, visual and culture studies. They constitute a network of crossed views on a subject which no serious reflection on globalization can do today.
- Full Text:
Was Myriophyllum spicatum L.(Haloragaceae) recently introduced to South Africa from Eurasia?
- Weyl, Philip S, Thum, RA, Moody, ML, Newman, RM, Coetzee, Julie A
- Authors: Weyl, Philip S , Thum, RA , Moody, ML , Newman, RM , Coetzee, Julie A
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/425463 , vital:72242 , xlink:href="https://doi.org/10.1016/j.aquabot.2015.09.003"
- Description: There is debate over the native or exotic status of Myriophyllum spicatum L. (Haloragaceae) in South Africa, which has important implications for developing and implementing management strategies. The aim of this study was to determine if M. spicatum was recently introduced from Eurasia by reconstructing the genetic relationships between South African and Eurasian M. spicatum using both a nuclear ribosomal (ITS1-5.8S-ITS2-26S) and a chloroplast intron (trnQ-rps16) sequence from 40 populations. For both these DNA markers, the South African populations were distinct from Eurasian populations, but always stemmed from a European origin. The data suggest that South African and European M. spicatum share a common ancestor, however the divergence of both markers are characteristic of a long period of isolation rather than a recent introduction from Europe. The genetic data from this study suggest that M. spicatum has not been introduced recently, but is most likely a native component of the South African flora.
- Full Text:
- Authors: Weyl, Philip S , Thum, RA , Moody, ML , Newman, RM , Coetzee, Julie A
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/425463 , vital:72242 , xlink:href="https://doi.org/10.1016/j.aquabot.2015.09.003"
- Description: There is debate over the native or exotic status of Myriophyllum spicatum L. (Haloragaceae) in South Africa, which has important implications for developing and implementing management strategies. The aim of this study was to determine if M. spicatum was recently introduced from Eurasia by reconstructing the genetic relationships between South African and Eurasian M. spicatum using both a nuclear ribosomal (ITS1-5.8S-ITS2-26S) and a chloroplast intron (trnQ-rps16) sequence from 40 populations. For both these DNA markers, the South African populations were distinct from Eurasian populations, but always stemmed from a European origin. The data suggest that South African and European M. spicatum share a common ancestor, however the divergence of both markers are characteristic of a long period of isolation rather than a recent introduction from Europe. The genetic data from this study suggest that M. spicatum has not been introduced recently, but is most likely a native component of the South African flora.
- Full Text:
Water service delivery in Harare: a willingness to pay (WTP) analysis
- Authors: Mugomba, Lynsey M
- Date: 2016
- Language: English
- Type: Thesis , Masters , MCom
- Identifier: http://hdl.handle.net/10962/4120 , vital:20614
- Description: In 2008-2009, Harare (Zimbabwe) was the centre of the worst cholera outbreak in Africa in the past fifteen years. A key reason cited was the lack of adequate water service delivery by the Harare City Council (HCC). Harare requires an optimum supply of 1 400 mega litres (ML) of water daily but the HCC has capacity to produce 650ML and after leakages and theft, only 400ML reaches consumers. This inadequacy compromised the hygiene of residents and forced them to resort to unsafe water sources. Coupled with a failing healthcare system, the outbreak resulted in over 4 000 deaths and further affected 100 000 people. The HCC attributes its poor service delivery to the lack of funds rendering them unable to adequately increase capacity and refurbish existing infrastructure (treatment plants and pipelines). This thesis serves to explore whether the residents of Harare (and surrounding satellite towns) would be willing to pay monthly contributions towards the USD$2.5 billion needed for various water capacity and infrastructure projects to ease the water crisis in Harare. The study analyses the water problem using a framework on the typical stages of water provision. The research also places an emphasis on the key social, economic and political factors that are contributing to the problem in Harare. Upon closer inspection, it was seen that the financial problems that the HCC is having are not only due to the economy, but poor management and transparency structures are also to blame. For various reasons, the government has largely lost its credibility with its citizens, leading some to conclude that the government’s actions reflect those of a predatory state. The contingent valuation method (willingness to pay-WTP) was used in conjunction with the dichotomous choice referendum. The binary probit model was used to help assess the degree to which different variables influenced the respondent’s decision to contribute to the needed funds. In spite of the seeming lack of trust, it was found that approximately 66.19% of the respondents were willing to pay. Amongst those willing, the mean willingness to pay amount was approximately USD$7 monthly per household.
- Full Text:
- Authors: Mugomba, Lynsey M
- Date: 2016
- Language: English
- Type: Thesis , Masters , MCom
- Identifier: http://hdl.handle.net/10962/4120 , vital:20614
- Description: In 2008-2009, Harare (Zimbabwe) was the centre of the worst cholera outbreak in Africa in the past fifteen years. A key reason cited was the lack of adequate water service delivery by the Harare City Council (HCC). Harare requires an optimum supply of 1 400 mega litres (ML) of water daily but the HCC has capacity to produce 650ML and after leakages and theft, only 400ML reaches consumers. This inadequacy compromised the hygiene of residents and forced them to resort to unsafe water sources. Coupled with a failing healthcare system, the outbreak resulted in over 4 000 deaths and further affected 100 000 people. The HCC attributes its poor service delivery to the lack of funds rendering them unable to adequately increase capacity and refurbish existing infrastructure (treatment plants and pipelines). This thesis serves to explore whether the residents of Harare (and surrounding satellite towns) would be willing to pay monthly contributions towards the USD$2.5 billion needed for various water capacity and infrastructure projects to ease the water crisis in Harare. The study analyses the water problem using a framework on the typical stages of water provision. The research also places an emphasis on the key social, economic and political factors that are contributing to the problem in Harare. Upon closer inspection, it was seen that the financial problems that the HCC is having are not only due to the economy, but poor management and transparency structures are also to blame. For various reasons, the government has largely lost its credibility with its citizens, leading some to conclude that the government’s actions reflect those of a predatory state. The contingent valuation method (willingness to pay-WTP) was used in conjunction with the dichotomous choice referendum. The binary probit model was used to help assess the degree to which different variables influenced the respondent’s decision to contribute to the needed funds. In spite of the seeming lack of trust, it was found that approximately 66.19% of the respondents were willing to pay. Amongst those willing, the mean willingness to pay amount was approximately USD$7 monthly per household.
- Full Text:
Water supply development decision-making in South Africa
- Authors: Preston, Ian Robert
- Date: 2016
- Subjects: Water security -- South Africa , Water resources development -- South Africa -- Cost effectiveness , Water consumption -- Economic aspects -- South Africa , Water-supply -- South Africa -- Management , Water-supply -- South Africa -- Decision making
- Language: English
- Type: Thesis , Masters , MCom
- Identifier: vital:1210 , http://hdl.handle.net/10962/d1020848
- Description: Balancing water demand and supply in South Africa involves high levels of uncertainty. The Department of Water and Sanitation (DWS) is responsible for making decisions to either increase water supply or decrease water demand so as to ensure that sufficient water is available, when and where it is needed. However, no retrospective analyses of such decisions have been found. One way to assess such decisions is to evaluate the associated costs and benefits thereof. Therefore the primary aim of this study is to evaluate the costs and benefits of selected water supply options, and of the decision-making associated with those options. In order to achieve this purpose, four case studies were analysed within a mixed-methods research paradigm, which used both quantitative and qualitative methods, including unit reference value (URV) analysis, inter- and intra-case analysis and content analysis to examine the success of the decisions made. The four case studies were conducted on the Inyaka, Nandoni, Berg and De Hoop dams and their catchments. Firstly, estimated and actual project costs were compared using unit reference analysis and inter-case analyses. Secondly, the reduction of mean annual runoff (MAR) caused by invasive alien plants (IAPs) and the cost of clearing them in the dam catchments were evaluated using inter-case analyses. Information thus gathered was used together with data from DWS documentation and the results of interviews with ten key specialists, to analyse the decision-making process that led to the decision to build De Hoop Dam (the most recent case study). The rational decision-making model (RDMM) was used as a framework within which to analyse and evaluate this decision-making process. This study has also demonstrated how the RDMM can be used to assess decision-making associated with water supply development. The results of this study show that there is considerable variation of estimated costs (at the time that the decision to build the dam was taken) in relation to the actual costs of building the dams and that Ministers were not put in a position to understand the full long-term costs or the opportunity costs of the proposed dams. Furthermore, the most recent IAP data (2008) shows that the impact on water security by IAPs could not offset the water security resulting from building each of the four dams. However, if IAP management is not continued in these catchments, the projected reduction of MAR by IAPs will compromise water security within 45 years. Given the almost exponential spread and densification of IAPs, together with their long-term impact on MAR and increased costs of controlling them, it is clear that IAP management should have been factored into water supply decision-making from the outset. In the analysis of the decision to build the De Hoop Dam, the results show that while the decision-making process that culminated in the decision to build the dam did not follow the steps of the RDMM, DWS appears to have followed a somewhat similar approach. It was found that while there was a need for the provision of additional water in the Olifants catchment, this need was overstated and the resulting overestimation caused the scale and size of the dam to be larger than it could and probably should have been. Additionally, it appears that DWS‘s decision to build the De Hoop Dam themselves, rather than having it built by the private sector, may have been less than optimal. It is recommended that, in future decision-making, DWS needs to incorporate multiple alternative options into the same solution, and to ensure that decision-makers are put into a position to make informed decisions, including adequate consideration of externalities. Furthermore, DWS needs to employ decision-making models such as the RDMM to facilitate retrospective analyses to improve their institutional knowledge. Keywords: water resources management, dams, invasive alien plants, decision-making, unit reference values, rational decision-making model.
- Full Text:
- Authors: Preston, Ian Robert
- Date: 2016
- Subjects: Water security -- South Africa , Water resources development -- South Africa -- Cost effectiveness , Water consumption -- Economic aspects -- South Africa , Water-supply -- South Africa -- Management , Water-supply -- South Africa -- Decision making
- Language: English
- Type: Thesis , Masters , MCom
- Identifier: vital:1210 , http://hdl.handle.net/10962/d1020848
- Description: Balancing water demand and supply in South Africa involves high levels of uncertainty. The Department of Water and Sanitation (DWS) is responsible for making decisions to either increase water supply or decrease water demand so as to ensure that sufficient water is available, when and where it is needed. However, no retrospective analyses of such decisions have been found. One way to assess such decisions is to evaluate the associated costs and benefits thereof. Therefore the primary aim of this study is to evaluate the costs and benefits of selected water supply options, and of the decision-making associated with those options. In order to achieve this purpose, four case studies were analysed within a mixed-methods research paradigm, which used both quantitative and qualitative methods, including unit reference value (URV) analysis, inter- and intra-case analysis and content analysis to examine the success of the decisions made. The four case studies were conducted on the Inyaka, Nandoni, Berg and De Hoop dams and their catchments. Firstly, estimated and actual project costs were compared using unit reference analysis and inter-case analyses. Secondly, the reduction of mean annual runoff (MAR) caused by invasive alien plants (IAPs) and the cost of clearing them in the dam catchments were evaluated using inter-case analyses. Information thus gathered was used together with data from DWS documentation and the results of interviews with ten key specialists, to analyse the decision-making process that led to the decision to build De Hoop Dam (the most recent case study). The rational decision-making model (RDMM) was used as a framework within which to analyse and evaluate this decision-making process. This study has also demonstrated how the RDMM can be used to assess decision-making associated with water supply development. The results of this study show that there is considerable variation of estimated costs (at the time that the decision to build the dam was taken) in relation to the actual costs of building the dams and that Ministers were not put in a position to understand the full long-term costs or the opportunity costs of the proposed dams. Furthermore, the most recent IAP data (2008) shows that the impact on water security by IAPs could not offset the water security resulting from building each of the four dams. However, if IAP management is not continued in these catchments, the projected reduction of MAR by IAPs will compromise water security within 45 years. Given the almost exponential spread and densification of IAPs, together with their long-term impact on MAR and increased costs of controlling them, it is clear that IAP management should have been factored into water supply decision-making from the outset. In the analysis of the decision to build the De Hoop Dam, the results show that while the decision-making process that culminated in the decision to build the dam did not follow the steps of the RDMM, DWS appears to have followed a somewhat similar approach. It was found that while there was a need for the provision of additional water in the Olifants catchment, this need was overstated and the resulting overestimation caused the scale and size of the dam to be larger than it could and probably should have been. Additionally, it appears that DWS‘s decision to build the De Hoop Dam themselves, rather than having it built by the private sector, may have been less than optimal. It is recommended that, in future decision-making, DWS needs to incorporate multiple alternative options into the same solution, and to ensure that decision-makers are put into a position to make informed decisions, including adequate consideration of externalities. Furthermore, DWS needs to employ decision-making models such as the RDMM to facilitate retrospective analyses to improve their institutional knowledge. Keywords: water resources management, dams, invasive alien plants, decision-making, unit reference values, rational decision-making model.
- Full Text:
Water Use and Food Security: Knowledge Dissemination and Use in Agricultural Colleges and Local Learning Networks for Homestead Food Gardening and Smallholder Farming
- Lotz-Sisitka, Heila, Pesanayi, Tichaona, Weaver, Kim, Lupele, Chisala, O’Donoghue, Rob B, Sithole, Phindile, van Staden, Wilna, Mabeza, Chris, Denison, C M Jonathan, Phillips, Katrina
- Authors: Lotz-Sisitka, Heila , Pesanayi, Tichaona , Weaver, Kim , Lupele, Chisala , O’Donoghue, Rob B , Sithole, Phindile , van Staden, Wilna , Mabeza, Chris , Denison, C M Jonathan , Phillips, Katrina
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , report
- Identifier: http://hdl.handle.net/10962/436825 , vital:73308 , ISBN 978-1-4312-0852-4 , https://wrcwebsite.azurewebsites.net/wp-content/uploads/mdocs/2277-1-16.pdf
- Description: This final report has detailed the work that went into pilot testing an Ac-tion Oriented Strategy (AOS) to support Agricultural Colleges to make use of the two sets of WRC materials that were the focus of the project. The general objective of this project entitled “Action oriented strategy for knowledge dissemination and training for skills development of water use in homestead food gardening and rain water harvesting for cropland food production” was: To develop a strategy for achieving effective knowledge dissemination and practical training to encourage productive water use for food crop production [amongst smallholder farmers and food growers in South Africa].
- Full Text:
- Authors: Lotz-Sisitka, Heila , Pesanayi, Tichaona , Weaver, Kim , Lupele, Chisala , O’Donoghue, Rob B , Sithole, Phindile , van Staden, Wilna , Mabeza, Chris , Denison, C M Jonathan , Phillips, Katrina
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , report
- Identifier: http://hdl.handle.net/10962/436825 , vital:73308 , ISBN 978-1-4312-0852-4 , https://wrcwebsite.azurewebsites.net/wp-content/uploads/mdocs/2277-1-16.pdf
- Description: This final report has detailed the work that went into pilot testing an Ac-tion Oriented Strategy (AOS) to support Agricultural Colleges to make use of the two sets of WRC materials that were the focus of the project. The general objective of this project entitled “Action oriented strategy for knowledge dissemination and training for skills development of water use in homestead food gardening and rain water harvesting for cropland food production” was: To develop a strategy for achieving effective knowledge dissemination and practical training to encourage productive water use for food crop production [amongst smallholder farmers and food growers in South Africa].
- Full Text:
Ways of seeing over time: the construction and imagination of ‘historic separation’ in Israeli and Palestinian cultures
- Authors: Butler, Nina Melissa
- Date: 2016
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/474 , vital:19962
- Description: There exists an international consensus that Palestinian and Israeli societies are ceaselessly and essentially acrimonious. This thesis argues that the conceptualisation of ‘historic separation’ in Palestine/Israel is supported and nourished by national narratives that follow classic historicism and a linear trajectory of essentialised culture progressing over time. Given these patterns in historiography and cultural expressions, conceptualisations of the future are argued to be dominated by the ‘overdetermined’ and ‘sacralised’ pasts that arrest the ability to conceive of alternative horizons. These national narratives are analysed borrowing from the theorisation of Edward Said on hegemonic culture, and Ranjit Guha’s Subaltern critique of historicism. Zionism is argued to function as a cultural hegemony that operates in a mercurial, selfsustaining and vibrant manner that has the effect of what this thesis terms ‘centrifugal magnetism’ on discourse in the region. Palestinian national narratives are held to be in tangential relation to Zionism (a classic colonial master-narrative), thus entering into a ‘terrible embrace’ of destructive colonial/postcolonial repetition that tends towards violent conflict and the discrimination of minorities. This thesis then proposes a ‘way out’ of this historiographical pattern that is argued to tangibly inform the cultural fabric of the region. By drawing on the later works of Mahmoud Darwish, Mustaffa Hallaj and Said, it is proposed that there are traces of a notion of self and community that can be described as postnational. This demands a reconstruction of narratives of the past in the region in a pluralistic fashion that is based upon shared exilic identity in flux over what Darwish termed an ‘open historical space’. Crucially, this alternative postnational narrative opens up conceptualisations of the future and is founded upon a renewed disposition to temporality. This thesis thus concludes by proposing that an understanding of temporality as ‘ecstatic’ and essential to being (Martin Heidegger) should be included as a crucial consideration for the end to conflict and the attainment of just and equitable futures.
- Full Text:
- Authors: Butler, Nina Melissa
- Date: 2016
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/474 , vital:19962
- Description: There exists an international consensus that Palestinian and Israeli societies are ceaselessly and essentially acrimonious. This thesis argues that the conceptualisation of ‘historic separation’ in Palestine/Israel is supported and nourished by national narratives that follow classic historicism and a linear trajectory of essentialised culture progressing over time. Given these patterns in historiography and cultural expressions, conceptualisations of the future are argued to be dominated by the ‘overdetermined’ and ‘sacralised’ pasts that arrest the ability to conceive of alternative horizons. These national narratives are analysed borrowing from the theorisation of Edward Said on hegemonic culture, and Ranjit Guha’s Subaltern critique of historicism. Zionism is argued to function as a cultural hegemony that operates in a mercurial, selfsustaining and vibrant manner that has the effect of what this thesis terms ‘centrifugal magnetism’ on discourse in the region. Palestinian national narratives are held to be in tangential relation to Zionism (a classic colonial master-narrative), thus entering into a ‘terrible embrace’ of destructive colonial/postcolonial repetition that tends towards violent conflict and the discrimination of minorities. This thesis then proposes a ‘way out’ of this historiographical pattern that is argued to tangibly inform the cultural fabric of the region. By drawing on the later works of Mahmoud Darwish, Mustaffa Hallaj and Said, it is proposed that there are traces of a notion of self and community that can be described as postnational. This demands a reconstruction of narratives of the past in the region in a pluralistic fashion that is based upon shared exilic identity in flux over what Darwish termed an ‘open historical space’. Crucially, this alternative postnational narrative opens up conceptualisations of the future and is founded upon a renewed disposition to temporality. This thesis thus concludes by proposing that an understanding of temporality as ‘ecstatic’ and essential to being (Martin Heidegger) should be included as a crucial consideration for the end to conflict and the attainment of just and equitable futures.
- Full Text: