Branch-length estimation bias misleads molecular dating for a vertebrate mitochondrial phylogeny

Despite recent methodological advances in inferring the time-scale of biological evolution from molecular data, the fundamental question of whether our substitution models are sufficiently well specified to accurately estimate branch-lengths has received little attention. I examine this implicit assumption of all molecular dating methods, on a vertebrate mitochondrial protein-coding dataset. Comparison with analyses in which the data are RY-coded (AG → R; CT → Y) suggests that even rates-across-sites maximum likelihood greatly under-compensates for multiple substitutions among the standard (ACGT) NT-coded data, which has been subject to greater phylogenetic signal erosion. Accordingly, the fossil record indicates that branch-lengths inferred from the NT-coded data translate into divergence time overestimates when calibrated from deeper in the tree. Intriguingly, RY-coding led to the opposite result. The underlying NT and RY substitution model misspecifications likely relate respectively to “hidden” rate heterogeneity and changes in substitution processes across the tree, for which I provide simulated examples. Given the magnitude of the inferred molecular dating errors, branch-length estimation biases may partly explain current conflicts with some palaeontological dating estimates.

Global civil society and adult education for social change : a postcolonial perspective

Adult education plays an important role in global economic development and features prominently in debates about changing requirements of post-industrial knowledge societies. This dominant technical-instrumental understanding of adult education in public discourse masks the transformative function of certain types of adult education - that is, the possibilities of adult education to improve social justice issues such as workers’ rights, human rights, civic participation in governance and socially just development. Given the increasing social stratification between and within the North and South in the global era, the potential of adult education to effect social change has been rediscovered by organisations within global civil society, namely international non-governmental organisations (INGOs). The broad objective of this research was to carry out an in-depth qualitative case study of a human rights advocacy program provided by a Northern INGO predominantly operating within the global South. The study analyses how participants see this program in terms of its potential to contribute to progressive social change in their home communities across the Asia-Pacific region. The following questions guided the study: 1. To what extent does this adult education program challenge existing systems of domination and marginalisation? 2. How did completion of the program affect participants’ views of their abilities to facilitate social action within their communities? Data sources for this research were interviews with 19 participants and staff and questionnaires from 28 participants of the program from a variety of countries in the Asia-pacific region. The gap in the literature that this study addressed is that existing empirical research sidelines the analysis of the globalisation, adult education, and social change nexus from a perspective that takes the marginalised other seriously, tending instead to mirror the material subjugation of the South in discursive practices. Social change is highly context-specific and strategies to advance it depend on the way in which people understand their reality and are affected by adverse social conditions. The present study employed a postcolonial framework that provided a holistic approach to analysing adult education for social change inclusive of material, political, and social conditions and the interplay between these from the local to the global level. The program convincingly exemplified an example of adult education for counter-hegemonic resistance against the dominant neoliberal discourse. It achieved this by enabling participants, based on Freirian pedagogical principles, to locate the problem of social change and frame their strategies to address it within mutually constitutive local and global developments and the discourses that describe them. It provided the underpinning knowledge and skills for effective advocacy and created opportunities to build networks between various stakeholders. At minimum, most advocates accord their participation in the program a supporting role in enhancing their ability to examine causes for social injustices and ways to address these. Some advocates even regarded their program participation as fundamental in understanding these issues. Almost all participants reported an increased skill-set that enabled them to become more effective advocates.

Corporate profit and impression management in developing markets

In this study, we examine how organisations in Fiji communicate or legitimise their profit. We base the need for understanding this phenomenon on the following premise. Organisations are part of a wider society, and in competition for scarce resources. Organisations obtain the rights to consume resources upon conception, but must continually legitimise their rights of existence and the need to access the resources. Legitimacy is the ability to continue to justify one’s authority to exist in a society. Organisations rights to resources are contractual, and have a moral obligation to act in a responsible manner and justify their outcomes, actions, and activities to external stakeholders. Such justifications would be an attempt at legitimizing their existence by some form of impression management. Impression management refers to the process by which individuals attempt to influence the impression of others (Melo et al. 2009). In corporate reporting, impression management occurs when management selects, display, and presents that information in a manner that distorts readers’ perceptions of corporate achievements (Neu 1991; Patten 2002), and is managed best through disclosures (O’Donovan 2002). In developing economies, there is significant Government protection that creates near-monopoly sectors and industries. The rendered protection permits organisations to provide essential services to the community at reasonable costs. Organisations in these sectors and industries have an ominous need to legitimise their position and actions. The bond between the organisations and the society is much stronger, making organisations devote more effort in communicating their activities. Protection permits organisations to make reasonable profits to sustain their operations. Society may not accept abnormal profits from operational efficiencies. Profit is fundamental to the society’s perception of an organisation, amplifying the need for the firm to justify a level of profit. Abnormal profit for organisations construes bad news, and organisations would make relevant disclosures to manage stakeholder impressions on profit (Patten 2002). Organisations can manage impressions by disclosing information in a particular way. That is, organisations would want to put the impression that the abnormal profit is justified and the society will obtain its benefits in future. Such form of impression management requires unambiguous disclosure of information. The readability of corporate disclosures is an important indicator of organisational abnormal profit-related legitimacy efforts in developing economies.

Modelling port water collision risk using traffic conflicts

Navigational collisions are one of the major safety concerns for many seaports. Despite the extent of work recently done on collision risk analysis in port waters, little is known about the influencing factors of the risk. This paper develops a technique for modeling collision risks in port waterways in order to examine the associations between the risks and the geometric, traffic, and regulatory control characteristics of waterways. A binomial logistic model, which accounts for the correlations in the risks of a particular fairway at different time periods, is derived from traffic conflicts and calibrated for the Singapore port fairways. Estimation results show that the fairways attached to shoreline, traffic intersection and international fairway attribute higher risks, whereas those attached to confined water and local fairway possess lower risks. Higher risks are also found in the fairways featuring higher degree of bend, lower depth of water, higher numbers of cardinal and isolated danger marks, higher density of moving ships and lower operating speed. The risks are also found to be higher for night-time conditions.

A fundamental numerical and theoretical study for the vibrational properties of nanowires

Based on the molecular dynamics (MD) simulation and the classical Euler-Bernoulli beam theory, a fundamental study of the vibrational performance of the Ag nanowire (NW) is carried out. A comprehensive analysis of the quality (Q)-factor, natural frequency, beat vibration, as well as high vibration mode is presented. Two excitation approaches, i.e., velocity excitation and displacement excitation, have been successfully implemented to achieve the vibration of NWs. Upon these two kinds of excitations, consistent results are obtained, i.e., the increase of the initial excitation amplitude will lead to a decrease to the Q-factor, and moderate plastic deformation could increase the first natural frequency. Meanwhile, the beat vibration driven by a single relatively large excitation or two uniform excitations in both two lateral directions is observed. It is concluded that the nonlinear changing trend of external energy magnitude does not necessarily mean a nonconstant Q-factor. In particular, the first order natural frequency of the Ag NW is observed to decrease with the increase of temperature. Furthermore, comparing with the predictions by Euler- Bernoulli beam theory, the MD simulation provides a larger and smaller first vibration frequencies for the clamped-clamped and clamped-free thin Ag NWs, respectively. Additionally, for thin NWs, the first order natural frequency exhibits a parabolic relationship with the excitation magnitudes. The frequencies of the higher vibration modes tend to be low in comparison to Euler-Bernoulli beam theory predictions. A combined initial excitation is proposed which is capable to drive the NW under a multi-mode vibration and arrows the coexistence of all the following low vibration modes. This work sheds lights on the better understanding of the mechanical properties of NWs and benefits the increasing utilities of NWs in diverse nano-electronic devices.

Analysis of involved parties in port water conflicts

With increasing rate of shipping traffic, the risk of collisions in busy and congested port waters is expected to rise. However, due to low collision frequencies it is difficult to analyze such risk in a sound statistical manner. This study aims at examining the occurrence of traffic conflicts in order to understand the characteristics of vessels involved in navigational hazards. A binomial logit model was employed to evaluate the association of vessel attributes and the kinematic conditions with conflict severity levels. Results show a positive association for vessels of small gross tonnage, overall vessel length, vessel height and draft with conflict risk. Conflicts involving a pair of dynamic vessels sailing at low speeds also have similar effects.

Analysis of marine conflicts

The traffic conflict technique (TCT) is a powerful technique applied in road traffic safety assessment as a surrogate of the traditional accident data analysis. It has subdued the conceptual and implemental weaknesses of the accident statistics. Although this technique has been applied effectively in road traffic, it has not been practised well in marine traffic even though this traffic system has some distinct advantages in terms of having a monitoring system. This monitoring system can provide navigational information as well as other geometric information of the ships for a larger study area over a longer time period. However, for implementing the TCT in the marine traffic system, it should be examined critically to suit the complex nature of the traffic system. This paper examines the suitability of the TCT to be applied to marine traffic and proposes a framework for a follow up comprehensive conflict study.

Proactive management of collision risks in port waters using navigational traffic conflicts

Navigational collisions are one of the major safety concerns in many seaports. To address this safety concern, a comprehensive and structured method of collision risk management is necessary. Traditionally management of port water collision risks has been relied on historical collision data. However, this collision-data-based approach is hampered by several shortcomings, such as randomness and rarity of collision occurrence leading to obtaining insufficient number of samples for a sound statistical analysis, insufficiency in explaining collision causation, and reactive approach to safety. A promising alternative approach that overcomes these shortcomings is the navigational traffic conflict technique that uses traffic conflicts as an alternative to the collision data. This paper proposes a collision risk management method by utilizing the principles of this technique. This risk management method allows safety analysts to diagnose safety deficiencies in a proactive manner, which, consequently, has great potential for managing collision risks in a fast, reliable and efficient manner.

Numerical techniques for the variable order time fractional diffusion equation

In this paper we consider the variable order time fractional diffusion equation. We adopt the Coimbra variable order (VO) time fractional operator, which defines a consistent method for VO differentiation of physical variables. The Coimbra variable order fractional operator also can be viewed as a Caputo-type definition. Although this definition is the most appropriate definition having fundamental characteristics that are desirable for physical modeling, numerical methods for fractional partial differential equations using this definition have not yet appeared in the literature. Here an approximate scheme is first proposed. The stability, convergence and solvability of this numerical scheme are discussed via the technique of Fourier analysis. Numerical examples are provided to show that the numerical method is computationally efficient. Crown Copyright © 2012 Published by Elsevier Inc. All rights reserved.

Privacy by design : Does it matter for social networks?

Privacy is an important component of freedom and plays a key role in protecting fundamental human rights. It is becoming increasingly difficult to ignore the fact that without appropriate levels of privacy, a person’s rights are diminished. Users want to protect their privacy - particularly in “privacy invasive” areas such as social networks. However, Social Network users seldom know how to protect their own privacy through online mechanisms. What is required is an emerging concept that provides users legitimate control over their own personal information, whilst preserving and maintaining the advantages of engaging with online services such as Social Networks. This paper reviews “Privacy by Design (PbD)” and shows how it applies to diverse privacy areas. Such an approach will move towards mitigating many of the privacy issues in online information systems and can be a potential pathway for protecting users’ personal information. The research has also posed many questions in need of further investigation for different open source distributed Social Networks. Findings from this research will lead to a novel distributed architecture that provides more transparent and accountable privacy for the users of online information systems.

Responsibilisation and Rights: Explorations in Comparative Youth Criminology

Studies of international youth justice, punishment and control are in their infancy but the issues of globalisation, transnationalisation, policy transfer and localisation are gradually being addressed. There also appears a growing demand in policy and pressure group circles in the UK to learn more about other jurisdictions in order to emulate ‘best practice’ and avoid the worst excesses of punitive populism. However, existing comparative work in this area rarely ventures much beyond country specific descriptions of historical development, powers and procedures. Statistical comparisons – predominantly of custody rates – are becoming more sophisticated but remain beset with problems of partial and inaccurate data collection. The extent to which different countries do things differently, and how and why such difference is maintained, remains a relatively unexcavated territory. This article suggests a conceptually comparative framework in which degrees of international, national and local convergence and divergence can begin to be revealed and assessed.

The Punitive Turn in Juvenile Justice: Cultures of Control and Rights of Compliance in Western Europe and the USA

Separate systems of justice for children and young people have always been beset by issues of contradiction and compromise. There is compelling evidence that such ambiguity is currently being `resolved' by a greater governmental resort to neo-conservative punitive and correctional interventions and a neo-liberal responsibilizing mentality in which the protection historically afforded to children is rapidly dissolving. This resurgent authoritarianism appears all the more anachronistic when it is set against the widely held commitment to act within the guidelines established by various children's rights conventions. Of note is the United Nations Convention on the Rights of the Child, frequently described as the most ratified human rights convention in the world, but lamentably also the most violated. Based on international research on juvenile custody rates and children's rights compliance in the USA and Western Europe, this article examines why and to what extent `American exceptionalism' might be permeating European nation states.