Error, Bias, and Long-Branch Attraction in Data for Two Chloroplast Photosystem Genes in Seed Plants

Sequences of two chloroplast photosystem genes, psaA and psbB, together comprising about 3,500 bp, were obtained for all five major groups of extant seed plants and several outgroups among other vascular plants. Strongly supported, but significantly conflicting, phylogenetic signals were obtained in parsimony analyses from partitions of the data into first and second codon positions versus third positions. In the former, both genes agreed on a monophyletic gymnosperms, with Gnetales closely related to certain conifers. In the latter, Gnetales are inferred to be the sister group of all other seed plants, with gymnosperms paraphyletic. None of the data supported the modern ‘‘anthophyte hypothesis,’’ which places Gnetales as the sister group of flowering plants. A series of simulation studies were undertaken to examine the error rate for parsimony inference. Three kinds of errors were examined: random error, systematic bias (both properties of finite data sets), and statistical inconsistency owing to long-branch attraction (an asymptotic property). Parsimony reconstructions were extremely biased for third-position data for psbB. Regardless of the true underlying tree, a tree in which Gnetales are sister to all other seed plants was likely to be reconstructed for these data. None of the combinations of genes or partitions permits the anthophyte tree to be reconstructed with high probability. Simulations of progressively larger data sets indicate the existence of long-branch attraction (statistical inconsistency) for third-position psbB data if either the anthophyte tree or the gymnosperm tree is correct. This is also true for the anthophyte tree using either psaA third positions or psbB first and second positions. A factor contributing to bias and inconsistency is extremely short branches at the base of the seed plant radiation, coupled with extremely high rates in Gnetales and nonseed plant outgroups. M. J. Sanderson,* M. F. Wojciechowski,*† J.-M. Hu,* T. Sher Khan,* and S. G. Brady

Research Monograph: Building Online Participatory Systems: Towards the Community Based Interactive Environmental Decision Support Systems

The importance of broadening community participation in environmental decision-making is widely recognized and lack of participation in this process appears to be a perennial problem. In this context, there have been calls from some academics for the more extensive use of geographic information systems (GIS) and distance learning technologies, accessible via the Internet, as a possible means to inform and empower communities. However, a number of problems exist. For instance, at present the scope for online interaction between policy-makers and citizens is currently limited. Contemporary web-based environmental information systems suffer from this lack of interactivity on the one hand and on the other hand from the apparent complexity for the lay user. This paper explores the issue of online community participation at the local level and attempts to construct a framework for a new (and potentially more effective) model of online participatory decision-making. The key components, system architecture and stages of such a model are introduced. This model, referred to as a ‘Community Based Interactive Environmental Decision Support System’, incorporates advanced information technologies, distance learning and community involvement tools which will be applied and evaluated in the field through a pilot project in Tokyo in the summer of 2002.

Research Monograph: Constructing online collaborative environmental decision making systems

The use of computing to support environmental planning and the development of land use models dates back to the late 1950s. The main thrust of computing applications, which by the early 1980s increasingly included the use of geospatial technologies, is their contribution to better planning and decision making. The computing tools and technologies are designed to enhance the planners’ capability to deal with complex environments and to plan for prosperous and livable communities. This paper examines the role of Information Technologies (IT) and particularly Internet Based Geographic Information Systems (Internet GIS) as spatial decision support systems to aid community based local decision making. The paper also covers the advantages and challenges of these internet based mapping applications and tools for collaborative decision making on the environment.

Research monograph : emergence of smart urban ecosystems : application of ICT for capacity building in environmental decision making

Since the industrial revolution, our world has experienced rapid and unplanned industrialization and urbanization. As a result, we have had to cope with serious environmental challenges. In this context, explanation of how smart urban ecosystems can emerge, gains a crucial importance. Capacity building and community involvement have always been the key issues in achieving sustainable development and enhancing urban ecosystems. By considering these, this paper looks at new approaches to increase public awareness of environmental decision making. This paper will discuss the role of Information and Communication Technologies (ICT), particularly Web-based Geographic Information Systems (Web-based GIS) as spatial decision support systems to aid public participatory environmental decision making. The paper also explores the potential and constraints of these web-based tools for collaborative decision making.

Decision Matrix Compared with Partnering Principles

The ideas for this CRC research project are based directly on Sidwell, Kennedy and Chan (2002). That research examined a number of case studies to identify the characteristics of successful projects. The findings were used to construct a matrix of best practice project delivery strategies. The purpose of this literature review is to test the decision matrix against established theory and best practice in the subject of construction project management.

Report on the Development and Validation of the Best Practice Decision Matrix

The Co-operative Research Centre for Construction Innovation (CRC-CI) is funding a project known as Value Alignment Process for Project Delivery. The project consists of a study of best practice project delivery and the development of a suite of products, resources and services to guide project teams towards the best procurement approach for a specific project or group of projects. These resources will be focused on promoting the principles that underlie best practice project delivery rather than simply identifying an off-the-shelf procurement system. This project builds on earlier work by Sidwell, Kennedy and Chan (2002), on re-engineering the construction delivery process, which developed a procurement framework in the form of a Decision Matrix

Procurement Case Study and Decision-making Strategies

Objectives The procurement research of Sydney Opera House FM Exemplar Project aims to develop innovative methods and guidelines for the procurement of FM services, applicable to iconic and / or performing arts centre facilities, or facilities with similar FM functions. The initial procurement report in June 2005 analysed the strategic objectives and operational requirements that provide ‘demand statements’ as evaluation criteria in the service procurement process. The subsequent interim procurement report in September 2005 discussed the elements contributing to the criteria for decision-making in the service procurement process. This procurement report concentrates on the research on procurement strategies and innovative methods using a case study approach. The objectives of this report are: • to investigate service procurement methods and process in iconic and/or performing arts centre facilities; • to showcase FM innovation in Sydney Opera House through a case study; • to establish a preliminary decision-making framework and guidelines for selection of appropriate FM procurement routes to provide a useful model for FM community. Findings Findings from this procurement research are presented as follows. • FM innovation and experience of Sydney Opera House • Innovative procurement methods and processes, drawn from a case study of Sydney Opera House as exemplar • An integrated performance framework to link maintenance service functions to high level organisational objective and strategies • Procurement methods and contract outcomes, focusing on building maintenance and cleaning services of Sydney Opera House • Multi-dimensional assessment of Service Providers • General decision-making strategies and guidelines for selection of appropriate FM procurement routes Further Research Whilst the Sydney Opera House case study emphasises the experience of Sydney Opera House, a study of procurement strategies and methods from published research and FM good practice will supply facilities managers with alternative procurement routes. Further research on the procurement theme will develop a final decision-making model for the procurement of FM services, drawn from the evaluation of the case study outcomes, as well as FM good practice and findings from current published research.

Investment decision framework for infrastructure asset management: a probability-based approach

Australia’s civil infrastructure assets of roads, bridges, railways, buildings and other structures are worth billions of dollars. Road assets alone are valued at around A$ 140 billion. As the condition of assets deteriorate over time, close to A$10 billion is spent annually in asset maintenance on Australia's roads, or the equivalent of A$27 million per day. To effectively manage road infrastructures, firstly, road agencies need to optimise the expenditure for asset data collection, but at the same time, not jeopardise the reliability in using the optimised data to predict maintenance and rehabilitation costs. Secondly, road agencies need to accurately predict the deterioration rates of infrastructures to reflect local conditions so that the budget estimates could be accurately estimated. And finally, the prediction of budgets for maintenance and rehabilitation must provide a certain degree of reliability. A procedure for assessing investment decision for road asset management has been developed. The procedure includes: • A methodology for optimising asset data collection; • A methodology for calibrating deterioration prediction models; • A methodology for assessing risk-adjusted estimates for life-cycle cost estimates. • A decision framework in the form of risk map

Nation & internation practices in decision support tools in road asset management

This document provides a review of international and national practices in investment decision support tools in road asset management. Efforts were concentrated on identifying analytic frameworks, evaluation methodologies and criteria adopted by current tools. Emphasis was also given to how current approaches support Triple Bottom Line decision-making. Benefit Cost Analysis and Multiple Criteria Analysis are principle methodologies in supporting decision-making in Road Asset Management. The complexity of the applications shows significant differences in international practices. There is continuing discussion amongst practitioners and researchers regarding to which one is more appropriate in supporting decision-making. It is suggested that the two approaches should be regarded as complementary instead of competitive means. Multiple Criteria Analysis may be particularly helpful in early stages of project development, say strategic planning. Benefit Cost Analysis is used most widely for project prioritisation and selecting the final project from amongst a set of alternatives. Benefit Cost Analysis approach is useful tool for investment decision-making from an economic perspective. An extension of the approach, which includes social and environmental externalities, is currently used in supporting Triple Bottom Line decision-making in the road sector. However, efforts should be given to several issues in the applications. First of all, there is a need to reach a degree of commonality on considering social and environmental externalities, which may be achieved by aggregating the best practices. At different decision-making level, the detail of consideration of the externalities should be different. It is intended to develop a generic framework to coordinate the range of existing practices. The standard framework will also be helpful in reducing double counting, which appears in some current practices. Cautions should also be given to the methods of determining the value of social and environmental externalities. A number of methods, such as market price, resource costs and Willingness to Pay, are found in the review. The use of unreasonable monetisation methods in some cases has discredited Benefit Cost Analysis in the eyes of decision makers and the public. Some social externalities, such as employment and regional economic impacts, are generally omitted in current practices. This is due to the lack of information and credible models. It may be appropriate to consider these externalities in qualitative forms in a Multiple Criteria Analysis. Consensus has been reached in considering noise and air pollution in international practices. However, Australia practices generally omitted these externalities. Equity is an important consideration in Road Asset Management. The considerations are either between regions, or social groups, such as income, age, gender, disable, etc. In current practice, there is not a well developed quantitative measure for equity issues. More research is needed to target this issue. Although Multiple Criteria Analysis has been used for decades, there is not a generally accepted framework in the choice of modelling methods and various externalities. The result is that different analysts are unlikely to reach consistent conclusions about a policy measure. In current practices, some favour using methods which are able to prioritise alternatives, such as Goal Programming, Goal Achievement Matrix, Analytic Hierarchy Process. The others just present various impacts to decision-makers to characterise the projects. Weighting and scoring system are critical in most Multiple Criteria Analysis. However, the processes of assessing weights and scores were criticised as highly arbitrary and subjective. It is essential that the process should be as transparent as possible. Obtaining weights and scores by consulting local communities is a common practice, but is likely to result in bias towards local interests. Interactive approach has the advantage in helping decision-makers elaborating their preferences. However, computation burden may result in lose of interests of decision-makers during the solution process of a large-scale problem, say a large state road network. Current practices tend to use cardinal or ordinal scales in measure in non-monetised externalities. Distorted valuations can occur where variables measured in physical units, are converted to scales. For example, decibels of noise converts to a scale of -4 to +4 with a linear transformation, the difference between 3 and 4 represents a far greater increase in discomfort to people than the increase from 0 to 1. It is suggested to assign different weights to individual score. Due to overlapped goals, the problem of double counting also appears in some of Multiple Criteria Analysis. The situation can be improved by carefully selecting and defining investment goals and criteria. Other issues, such as the treatment of time effect, incorporating risk and uncertainty, have been given scant attention in current practices. This report suggested establishing a common analytic framework to deal with these issues.

Strategy for the development of investment decision-making framework for road asset management for queensland department of main roads

The aim of this project is to develop a systematic investment decision-making framework for infrastructure asset management by incorporation economic justification, social and environmental consideration in the decision-making process. This project assesses the factors that are expected to provide significant impacts on the variability of expenditures. A procedure for assessing risk and reliability for project investment appraisals will be developed. The project investigates public perception, social and environmental impacts on road infrastructure investment. This research will contribute to the debate about how important social and environmental issues should be incorporated into the investment decision-making process for infrastructure asset management.

International practices in investment decision making in road sector

This document provides the findings of an international review of investment decision-making practices in road asset management. Efforts were concentrated on identifying the strategic objectives of agencies in road asset management, establishing and understanding criteria different organisations adopted and ascertaining the exact methodologies used by different countries and international organisations. Road assets are powerful drivers of economic development and social equity. They also have significant impacts on the natural and man-made environment. The traditional definition of asset management is “A systematic process of maintaining, upgrading and operating physical assets cost effectively. It combines engineering principles with sound business practices and economic theory and it provides tools to facilitate a more organised, logical approach to decision-making” (US Dept. of Transportation, 1999). In recent years, the concept has been broadened to cover the complexity of decision making, based on a wider variety of policy considerations as well as social and environmental issues rather than is covered by Benefit-Cost analysis and pure technical considerations. Current international practices are summarised in table 2. It was evident that Engineering-economic analysis methods are well advanced to support decision-making. A range of tools available supports performance predicting of road assets and associated cost/benefit in technical context. The need for considering triple plus one bottom line of social, environmental and economic as well as political factors in decision-making is well understood by road agencies around the world. The techniques used to incorporate these however, are limited. Most countries adopt a scoring method, a goal achievement matrix or information collected from surveys. The greater uncertainty associated with these non-quantitative factors has generally not been taken into consideration. There is a gap between the capacities of the decision-making support systems and the requirements from decision-makers to make more rational and transparent decisions. The challenges faced in developing an integrated decision making framework are both procedural and conceptual. In operational terms, the framework should be easy to be understood and employed. In philosophical terms, the framework should be able to deal with challenging issues, such as uncertainty, time frame, network effects, model changes, while integrating cost and non-cost values into the evaluation. The choice of evaluation techniques depends on the feature of the problem at hand, on the aims of the analysis, and on the underlying information base At different management levels, the complexity in considering social, environmental, economic and political factor in decision-making is different. At higher the strategic planning level, more non-cost factors are involved. The complexity also varies based on the scope of the investment proposals. Road agencies traditionally place less emphasis on evaluation of maintenance works. In some cases, social equity, safety, environmental issues have been used in maintenance project selection. However, there is not a common base for the applications.

National practices in investment decision making in road sector

This document provides the findings of a national review of investment decision-making practices in road asset management. Efforts were concentrated on identifying the strategic objectives of agencies in road asset management, establishing and understanding criteria different organisations adopted and ascertaining the exact methodologies used by different sate road authorities. The investment objectives of Australian road authorities are based on triple-bottom line considerations (social, environmental, economic and political). In some cases, comparing with some social considerations, such as regional economic development, equity, and access to pubic service etc., Benefit-Cost Ratio has limited influence on the decision-making. Australian road authorities have developed various decision support tools. Although Multi-Criteria Analysis has been preliminarily used in case by case study, pavement management systems, which are primarily based on Benefit Cost Analysis, are still the main decision support tool. This situation is not compatible with the triple-bottom line objectives. There is need to fill the gap between decision support tools and decision-making itself. Different decision criteria should be adopted based on the contents of the work. Additional decision criteria, which are able to address social, environmental and political impacts, are needed to develop or identify. Environmental issue plays a more and more important role in decision-making. However, the criteria and respective weights in decision-making process are yet to be clearly identified. Social and political impacts resulted from road infrastructure investment can be identified through Community Perceptions Survey. With accumulative data, prediction models, which are similar as pavement performance models, can be established. Using these models, the decision-makers are able to foresee the social and political consequences of investment alternatives.

Investment decision-making under risk (reliability) and uncertainty for infrastructure asset management

Risks and uncertainties are inevitable in engineering projects and infrastructure investments. Decisions about investment in infrastructure such as for maintenance, rehabilitation and construction works can pose risks, and may generate significant impacts on social, cultural, environmental and other related issues. This report presents the results of a literature review of current practice in identifying, quantifying and managing risks and predicting impacts as part of the planning and assessment process for infrastructure investment proposals. In assessing proposals for investment in infrastructure, it is necessary to consider social, cultural and environmental risks and impacts to the overall community, as well as financial risks to the investor. The report defines and explains the concept of risk and uncertainty, and describes the three main methodology approaches to the analysis of risk and uncertainty in investment planning for infrastructure, viz examining a range of scenarios or options, sensitivity analysis, and a statistical probability approach, listed here in order of increasing merit and complexity. Forecasts of costs, benefits and community impacts of infrastructure are recognised as central aspects of developing and assessing investment proposals. Increasingly complex modelling techniques are being used for investment evaluation. The literature review identified forecasting errors as the major cause of risk. The report contains a summary of the broad nature of decision-making tools used by governments and other organisations in Australia, New Zealand, Europe and North America, and shows their overall approach to risk assessment in assessing public infrastructure proposals. While there are established techniques to quantify financial and economic risks, quantification is far less developed for political, social and environmental risks and impacts. The report contains a summary of the broad nature of decision-making tools used by governments and other organisations in Australia, New Zealand, Europe and North America, and shows their overall approach to risk assessment in assessing public infrastructure proposals. While there are established techniques to quantify financial and economic risks, quantification is far less developed for political, social and environmental risks and impacts. For risks that cannot be readily quantified, assessment techniques commonly include classification or rating systems for likelihood and consequence. The report outlines the system used by the Australian Defence Organisation and in the Australian Standard on risk management. After each risk is identified and quantified or rated, consideration can be given to reducing the risk, and managing any remaining risk as part of the scope of the project. The literature review identified use of risk mapping techniques by a North American chemical company and by the Australian Defence Organisation. This literature review has enabled a risk assessment strategy to be developed, and will underpin an examination of the feasibility of developing a risk assessment capability using a probability approach.

Decision support tools for concrete infrastructure rehabilitation (using FRP composites)

This report presents a summary of the research conducted by the research team of the CRC project 2002-005-C, “Decision support tools for concrete infrastructure rehabilitation”. The project scope, objectives, significance and innovation and the research methodology is outlined in the introduction, which is followed by five chapters covering different aspects of the research completed. Major findings of a review of literature conducted covering both use of fibre reinforced polymer composites in rehabilitation of concrete bridge structures and decision support frameworks in civil infrastructure asset management is presented in chapter two. Case study of development of a strengthening scheme for the “Tenthill Creek bridge” is covered in the third chapter, which summarises the capacity assessment, traditional strengthening solution and the innovative solution using FRP composites. The fourth chapter presents the methodology for development of a user guide covering selection of materials, design and application of FRP in strengthening of concrete structures, which were demonstrated using design examples. Fifth chapter presents the methodology developed for evaluating whole of life cycle costing of treatment options for concrete bridge structures. The decision support software tool developed to compare different treatment options based on reliability based whole of life cycle costing will be briefly described in this chapter as well. The report concludes with a summary of findings and recommendations for future research.