Synthesizing and databasing fossil calibrations: divergence dating and beyond

Divergence dating studies, which combine temporal data from the fossil record with branch length data from molecular phylogenetic trees, represent a rapidly expanding approach to understanding the history of life. National Evolutionary Synthesis Center hosted the first Fossil Calibrations Working Group (3–6 March, 2011, Durham, NC, USA), bringing together palaeontologists, molecular evolutionists and bioinformatics experts to present perspectives from disciplines that generate, model and use fossil calibration data. Presentations and discussions focused on channels for interdisciplinary collaboration, best practices for justifying, reporting and using fossil calibrations and roadblocks to synthesis of palaeontological and molecular data. Bioinformatics solutions were proposed, with the primary objective being a new database for vetted fossil calibrations with linkages to existing resources, targeted for a 2012 launch.

The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography

The ratite moa (Aves: Dinornithiformes) were a speciose group of massive graviportal avian herbivores that dominated the New Zealand (NZ) ecosystem until their extinction �600 years ago. The phylogeny and evolutionary history of this morphologically diverse order has remained controversial since their initial description in 1839. We synthesize mitochondrial phylogenetic information from 263 subfossil moa specimens from across NZ with morphological, ecological, and new geological data to create the first comprehensive phylogeny, taxonomy, and evolutionary timeframe for all of the species of an extinct order. We also present an important new geological/paleogeographical model of late Cenozoic NZ, which suggests that terrestrial biota on the North and South Island landmasses were isolated for most of the past 20–30 Ma. The data reveal that the patterns of genetic diversity within and between differentmoaclades reflect a complex history following a major marine transgression in the Oligocene, affected by marine barriers, tectonic activity, and glacial cycles. Surprisingly, the remarkable morphological radiation of moa appears to have occurred much more recently than previous early Miocene (ca. 15 Ma) estimates, and was coincident with the accelerated uplift of the Southern Alps just ca. 5–8.5 Ma. Together with recent fossil evidence, these data suggest that the recent evolutionary history of nearly all of the iconic NZ terrestrial biota occurred principally on just the South Island.

Late Oligocene to middle Miocene rifting and syn-extensional magmatism in the southwestern Sierra Madre occidental, Mexico: the beginning of the Gulf of California rift

Although Basin and Range style extension affected several areas of western Mexico since the Late Eocene, extension in the Gulf of California region (the Gulf Extensional Province GEP) is thought to have started as subduction waned and ended at ~14 12.5 Ma. A general consensus also exists in considering the mid Miocene Comondú group as a suprasubduction volcanic arc. Our new integration of the geology of the south east Gulf region, backed by 43 new Ar Ar and U Pb mineral ages and geochemical studies, document a widespread phase of extension in the southern GEP between latest Oligocene and Early Miocene that subsequently focused in the region of the future Gulf in the Middle Miocene. Upper Oligocene to Lower Miocene rocks across the southern Sierra Madre Occidental (SMO)(northern Nayarit and southern Sinaloa) were affected by major ~N S to NNW striking normal faults prior to ~21 Ma. Then, between ~21 and 11 Ma, a system of NNW-SSE high angle extensional faults continued extending the southwestern side of the SMO. Rhyolitic domes, shallow intrusive bodies, and lesser basalts were emplaced along this extensional belt at 20-17 Ma. In northern Sinaloa, large grabens were floored by huge dome complexes at ~21-17 Ma and filled by continental sediments with interlayered basalts dated at 15-14 Ma, a setting and timing very similar to Sonora. Early to Middle Miocene volcanism, including the largely volcaniclastic Comondú strata in Baja California Sur, was thus emplaced in rift basins and was likely associated to decompression melting of upper mantle (inducing crustal partial melting) rather than to fluxing by fluids from the young subducting plate. Along the Nayarit and Sinaloa coast, flatlying basaltic lava flows dated at 11-10 Ma are exposed just above the present sea level. Here, crustal thickness is almost half that in the unextended core of the SMO, implying significant lithosphere stretching before ~11 Ma. Our study shows that rifting began much earlier than Late Miocene and provided a fundamental control on the style and composition of volcanism from at least 30 Ma. We envision a sustained period of lithospheric stretching and magmatism during which the pace and breadth of extension changed at ~20-18 Ma to be narrower and likely more rapid, and again at ~12.5 Ma, when the kinematics of rifting became more oblique.

Late Oligocene to Middle Miocene rifting and synextensional magmatism in the southwestern Sierra Madre Occidental, Mexico : the beginning of the Gulf of California rift

Although Basin and Range–style extension affected large areas of western Mexico after the Late Eocene, most consider that extension in the Gulf of California region began as subduction waned and ended ca. 14–12.5 Ma. A general consensus also exists in considering Early and Middle Miocene volcanism of the Sierra Madre Occidental and Comondú Group as subduction related, whereas volcanism after ca. 12.5 Ma is extension related. Here we present a new regional geologic study of the eastern Gulf of California margin in the states of Nayarit and Sinaloa, Mexico, backed by 43 new Ar-Ar and U-Pb mineral ages, and geochemical data that document an earlier widespread phase of extension. This extension across the southern and central Gulf Extensional Province began between Late Oligocene and Early Miocene time, but was focused in the region of the future Gulf of California in the Middle Miocene. Late Oligocene to Early Miocene rocks across northern Nayarit and southern Sinaloa were affected by major approximately north-south– to north-northwest– striking normal faults prior to ca. 21 Ma. Between ca. 21 and 11 Ma, a system of north-northwest–south-southeast high angle extensional faults continued extending the southwestern side of the Sierra Madre Occidental. Rhyolitic domes, shallow intrusive bodies, and lesser basalts were emplaced along this extensional belt at 20–17 Ma. Rhyolitic rocks, in particular the domes and lavas, often show strong antecrystic inheritance but only a few Mesozoic or older xenocrysts, suggesting silicic magma generation in the mid-upper crust triggered by an extension induced basaltic infl ux. In northern Sinaloa, large grabens were occupied by huge volcanic dome complexes ca. 21–17 Ma and filled by continental sediments with interlayered basalts dated as 15–14 Ma, a stratigraphy and timing very similar to those found in central Sonora (northeastern Gulf of California margin). Early to Middle Miocene volcanism occurred thus in rift basins, and was likely associated with decompression melting of upper mantle (inducing crustal partial melting) rather than with fluxing by fluids from the young and slow subducting microplates. Along the eastern side of the Gulf of California coast, from Farallón de San Ignacio island offshore Los Mochis, Sinaloa, to San Blas, Nayarit, a strike distance of >700 km, flat lying basaltic lavas dated as ca. 11.5–10 Ma are exposed just above the present sea level. Here crustal thickness is almost half that in the unextended core of the adjacent Sierra Madre Occidental, implying signifi cant lithosphere stretching before ca. 11 Ma. This mafic pulse, with subdued Nb-Ta negative spikes, may be related to the detachment of the lower part of the subducted slab, allowing an upward asthenospheric flow into an upper mantle previously modified by fluid fluxes related to past subduction. Widespread eruption of very uniform oceanic island basalt–like lavas occurred by the late Pliocene and Pleistocene, only 20 m.y. after the onset of rifting and ~9 m.y. after the end of subduction, implying that preexisting subduction-modified mantle had now become isolated from melt source regions. Our study shows that rifting across the southern-central Gulf Extensional Province began much earlier than the Late Miocene and provided a fundamental control on the style and composition of volcanism from at least 30 Ma. We envision a sustained period of lithospheric stretching and magmatism during which the pace and breadth of extension changed ca. 20–18 Ma to be narrower, and again after ca. 12.5 Ma, when the kinematics of rifting became more oblique.

The impact of a congestion charging exemption on the demand for new low‐emission vehicles

Numerous initiatives have been employed around the world in order to address rising greenhouse gas (GHG) emissions originating from the transport sector. These measures include: travel demand management (congestion‐charging), increased fuel taxes, alternative fuel subsidies and low‐emission vehicle (LEV) rebates. Incentivizing the purchase of LEVs has been one of the more prevalent approaches in attempting to tackle this global issue. LEVs, whilst having the advantage of lower emissions and, in some cases, more efficient fuel consumption, also bring the downsides of increased purchase cost, reduced convenience of vehicle fuelling, and operational uncertainty. To stimulate demand in the face of these challenges, various incentive‐based policies, such as toll exemptions, have been used by national and local governments to encourage the purchase of these types of vehicles. In order to address rising GHG emissions in Stockholm, and in line with the Swedish Government’s ambition to operate a fossil free fleet by 2030, a number of policies were implemented targeting the transport sector. Foremost amongst these was the combination of a congestion charge – initiated to discourage emissions‐intensive travel – and an exemption from this charge for some LEVs, established to encourage a transition towards a ‘green’ vehicle fleet. Although both policies shared the aim of reducing GHG emissions, the exemption for LEVs carried the risk of diminishing the effectiveness of the congestion charging scheme. As the number of vehicle owners choosing to transition to an eligible LEV increased, the congestion‐reduction effectiveness of the charging scheme weakened. In fact, policy makers quickly recognized this potential issue and consequently phased out the LEV exemption less than 18 months after its introduction (1). Several studies have investigated the demand for LEVs through stated‐preference (SP) surveys across multiple countries, including: Denmark (2), Germany (3, 4), UK (5), Canada (6), USA (7, 8) and Australia (9). Although each of these studies differed in approach, all involved SP surveys where differing characteristics between various types of vehicles, including LEVs, were presented to respondents and these respondents in turn made hypothetical decisions about which vehicle they would be most likely to purchase. Although these studies revealed a number of interesting findings in regards to the potential demand for LEVs, they relied on SP data. In contrast, this paper employs an approach where LEV choice is modelled by taking a retrospective view and by using revealed preference (RP) data. By examining the revealed preferences of vehicle owners in Stockholm, this study overcomes one of the principal limitations of SP data, namely that stated preferences may not in fact reflect individuals’ actual choices, such as when cost, time, and inconvenience factors are real rather than hypothetical. This paper’s RP approach involves modelling the characteristics of individuals who purchased new LEVs, whilst estimating the effect of the congestion charging exemption upon choice probabilities and subsequent aggregate demand. The paper contributes to the current literature by examining the effectiveness of a toll exemption under revealed preference conditions, and by assessing the total effect of the policy based on key indicators for policy makers, including: vehicle owner home location, commuting patterns, number of children, age, gender and income. Extended Abstract Submission for Kuhmo Nectar Conference 2014 2 The two main research questions motivating this study were:  Which individuals chose to purchase a new LEV in Stockholm in 2008?; and,  How did the congestion charging exemption affect the aggregate demand for new LEVs in Stockholm in 2008? In order to answer these research questions the analysis was split into two stages. Firstly, a multinomial logit (MNL) model was used to identify which demographic characteristics were most significantly related to the purchase of an LEV over a conventional vehicle. The three most significant variables were found to be: intra‐cordon residency (positive); commuting across the cordon (positive); and distance of residence from the cordon (negative). In order to estimate the effect of the exemption policy on vehicle purchase choice, the model included variables to control for geographic differences in preferences, based on the location of the vehicle owners’ homes and workplaces in relation to the congestion‐charging cordon boundary. These variables included one indicator representing commutes across the cordon and another indicator representing intra‐cordon residency. The effect of the exemption policy on the probability of purchasing LEVs was estimated in the second stage of the analysis by focusing on the groups of vehicle owners that were most likely to have been affected by the policy i.e. those commuting across the cordon boundary (in both directions). Given the inclusion of the indicator variable representing commutes across the cordon, it is assumed that the estimated coefficient of this variable captures the effect of the exemption policy on the utility of choosing to purchase an exempt LEV for these two groups of vehicle owners. The intra‐cordon residency indicator variable also controls for differences between the two groups, based upon direction of travel across the cordon boundary. A counter‐hypothesis to this assumption is that the coefficient of the variable representing commuting across the cordon boundary instead only captures geo‐demographic differences that lead to variations in LEV ownership across the different groups of vehicle owners in relation to the cordon boundary. In order to address this counter‐hypothesis, an additional analysis was performed on data from a city with a similar geodemographic pattern to Stockholm, Gothenburg ‐ Sweden’s second largest city. The results of this analysis provided evidence to support the argument that the coefficient of the variable representing commutes across the cordon was capturing the effect of the exemption policy. Based upon this framework, the predicted vehicle type shares were calculated using the estimated coefficients of the MNL model and compared with predicted vehicle type shares from a simulated scenario where the exemption policy was inactive. This simulated scenario was constructed by setting the coefficient for the variable representing commutes across the cordon boundary to zero for all observations to remove the utility benefit of the exemption policy. Overall, the procedure of this second stage of the analysis led to results showing that the exemption had a substantial effect upon the probability of purchasing and aggregate demand for exempt LEVs in Stockholm during 2008. By making use of unique evidence of revealed preferences of LEV owners, this study identifies the common characteristics of new LEV owners and estimates the effect of Stockholm's congestion charging exemption upon the demand for new LEVs during 2008. It was found that the variables that had the greatest effect upon the choice of purchasing an exempt LEV included intra‐cordon residency (positive), distance of home from the cordon (negative), and commuting across the cordon (positive). It was also determined that owners under the age of 30 years preferred non‐exempt LEVs (low CO2 LEVs), whilst those over the age of 30 years preferred electric vehicles. In terms of electric vehicles, it was apparent that those individuals living within the city had the highest propensity towards purchasing this vehicle type. A negative relationship between choosing an electric vehicle and the distance of an individuals’ residency from the cordon was also evident. Overall, the congestion charging exemption was found to have increased the share of exempt LEVs in Stockholm by 1.9%, with, as expected, a much stronger effect on those commuting across the boundary, with those living inside the cordon having a 13.1% increase, and those owners living outside the cordon having a 5.0% increase. This increase in demand corresponded to an additional 538 (+/‐ 93; 95% C.I.) new exempt LEVs purchased in Stockholm during 2008 (out of a total of 5 427; 9.9%). Policy makers can take note that an incentive‐based policy can increase the demand for LEVs and appears to be an appropriate approach to adopt when attempting to reduce transport emissions through encouraging a transition towards a ‘green’ vehicle fleet.

Review: "Measuring and evaluating sustainability : ethics in sustainability indexes" by Sarah E. Fredericks, New York, Routledge, Routledge Studies in Sustainable Development, 2014

The concept of ‘sustainability’ has been pushed to the forefront of policy-making and politics as the world wakes up to the impacts of climate change and the effects of the rapid urbanisation and modern urban lifestyles (Yigitcanlar and Teriman 2014). Climate change and fossil fuel-based energy policy have emerged as the biggest challenges for our planet, threatening both built and natural systems with long-term consequences. However, the threats are not limited to the impacts of climate change and unsustainable energy system only – e.g., impacts of rapid urbanisation, socioeconomic crises and governance hiccups are just to name a few (Yigitcanlar 2010a). Along with these challenges, successfully coping with the enormous transformations that our cities, societies and the environment have been going through during the last few decades, and their...

Braving a New World : Design Interventions for Changing Climates. Papers from the Subtropical Cities 2013 Fall Conference of the Association of Collegiate Schools of Architecture (ACSA)

We no longer have the luxury of time as the effects of climate change are being felt, according to the latest Intergovernmental Panel on Climate Change report, on every continent and in every ocean. More than 50% of the population of the United States and 85% of Australians live in coastal regions. The number of people living in the world’s coastal regions is expected to increase along with the need to improve capacity to mitigate hazards , and manage the multiple risks that have been identified by the scientific community. Under the auspices of the Association of Collegiate Schools of Architecture (ACSA) design academics and practitioners from the Americas, Asia, and Australia met in Fort Lauderdale, Florida for the fourth Subtropical Cities international conference to share outcomes of research and new pedagogies to address the critical transformation of the physical environments and infrastructures of the world’s vulnerable coastal communities. The theme of Subtropical Cities, adopted by the ACSA for its Fall 2014 Conference, is not confined entirely to a latitudinal or climatic frame of reference. The paper and project presentations addressed a range of theoretical, practice-led, and education-oriented research topics in architecture and urban design related to the subtropics, with emphasis on urban and coastal regions. More than half the papers originate from universities and practices in coastal regions. Threads emerged from a tapestry of localized investigations to reveal a more global understanding about possible futures we are designing for current and future generations. The one hundred-plus conference delegates and presenters represented 33 universities and institutions from across the United States, Mexico, Canada, Australia, the Middle East, Peru and China. Case studies from India, Morocco, Tahiti, Indonesia, Jordan, and Cambodia were also presented, expanding the global knowledge base. Co-authored submissions presented new directions for architecture and design, with a resounding theme of collaboration across diverse disciplines. The ability to deal with abstraction and complexity, and the capacity to develop synthesis and frameworks for defining problem boundaries can be considered key attributes of architectural thinking. Such a unique set of abilities can forge collaboration with different professional disciplines to achieve extraordinary outcomes. As the broad range of papers presented at this conference suggest, existing architectural and urban typologies and practices are increasingly considered part of the cause and not the solution to adapting to climate change and sea level rise. Design responses and the actions needed to generate new and unfamiliar forms of urbanism and infrastructure for defense, adaptation, and retreat in subtropical urban regions are being actively explored in academic design studios and research projects around the world. Many presentations propose provocative and experimental strategies as global climate moves beyond our “comfort zone”. The ideas presented at the Subtropical Cities conference are timely as options for low-energy passive climatic design are becoming increasingly limited in the context of changing climate. At the same time, ways of reducing or obsoleting energy intensive mechanical systems in densely populated urban centres present additional challenges for designers and communities as a whole. The conference was marked by a common theme of trans-disciplinary research, where design integration with emerging technologies resonate with a reaffirmation of the centrality of design thinking, expanding the scope of the traditional architecture studio pedagogy to integrate knowledge from other disciplines and the participation of diverse communities.

Inventing life: Intellectual property and the new biology

In 2009, the National Research Council of the National Academies released a report on A New Biology for the 21st Century. The council preferred the term ‘New Biology’ to capture the convergence and integration of the various disciplines of biology. The National Research Council stressed: ‘The essence of the New Biology, as defined by the committee, is integration—re-integration of the many sub-disciplines of biology, and the integration into biology of physicists, chemists, computer scientists, engineers, and mathematicians to create a research community with the capacity to tackle a broad range of scientific and societal problems.’ They define the ‘New Biology’ as ‘integrating life science research with physical science, engineering, computational science, and mathematics’. The National Research Council reflected: 'Biology is at a point of inflection. Years of research have generated detailed information about the components of the complex systems that characterize life––genes, cells, organisms, ecosystems––and this knowledge has begun to fuse into greater understanding of how all those components work together as systems. Powerful tools are allowing biologists to probe complex systems in ever greater detail, from molecular events in individual cells to global biogeochemical cycles. Integration within biology and increasingly fruitful collaboration with physical, earth, and computational scientists, mathematicians, and engineers are making it possible to predict and control the activities of biological systems in ever greater detail.' The National Research Council contended that the New Biology could address a number of pressing challenges. First, it stressed that the New Biology could ‘generate food plants to adapt and grow sustainably in changing environments’. Second, the New Biology could ‘understand and sustain ecosystem function and biodiversity in the face of rapid change’. Third, the New Biology could ‘expand sustainable alternatives to fossil fuels’. Moreover, it was hoped that the New Biology could lead to a better understanding of individual health: ‘The New Biology can accelerate fundamental understanding of the systems that underlie health and the development of the tools and technologies that will in turn lead to more efficient approaches to developing therapeutics and enabling individualized, predictive medicine.’ Biological research has certainly been changing direction in response to changing societal problems. Over the last decade, increasing awareness of the impacts of climate change and dwindling supplies of fossil fuels can be seen to have generated investment in fields such as biofuels, climate-ready crops and storage of agricultural genetic resources. In considering biotechnology’s role in the twenty-first century, biological future-predictor Carlson’s firm Biodesic states: ‘The problems the world faces today – ecosystem responses to global warming, geriatric care in the developed world or infectious diseases in the developing world, the efficient production of more goods using less energy and fewer raw materials – all depend on understanding and then applying biology as a technology.’ This collection considers the roles of intellectual property law in regulating emerging technologies in the biological sciences. Stephen Hilgartner comments that patent law plays a significant part in social negotiations about the shape of emerging technological systems or artefacts: 'Emerging technology – especially in such hotbeds of change as the life sciences, information technology, biomedicine, and nanotechnology – became a site of contention where competing groups pursued incompatible normative visions. Indeed, as people recognized that questions about the shape of technological systems were nothing less than questions about the future shape of societies, science and technology achieved central significance in contemporary democracies. In this context, states face ongoing difficulties trying to mediate these tensions and establish mechanisms for addressing problems of representation and participation in the sociopolitical process that shapes emerging technology.' The introduction to the collection will provide a thumbnail, comparative overview of recent developments in intellectual property and biotechnology – as a foundation to the collection. Section I of this introduction considers recent developments in United States patent law, policy and practice with respect to biotechnology – in particular, highlighting the Myriad Genetics dispute and the decision of the Supreme Court of the United States in Bilski v. Kappos. Section II considers the cross-currents in Canadian jurisprudence in intellectual property and biotechnology. Section III surveys developments in the European Union – and the interpretation of the European Biotechnology Directive. Section IV focuses upon Australia and New Zealand, and considers the policy responses to the controversy of Genetic Technologies Limited’s patents in respect of non-coding DNA and genomic mapping. Section V outlines the parts of the collection and the contents of the chapters.

New dimeric supramolecular structure of mixed (phthalocyaninato)(porphyrinato)-europium(III) sandwiches : preparation and spectroscopic characteristics

The mixed double-decker Eu\[Pc(15C5)4](TPP) (1) was obtained by base-catalysed tetramerisation of 4,5-dicyanobenzo-15-crown-5 using the half-sandwich complex Eu(TPP)(acac) (acac = acetylacetonate), generated in situ, as the template. For comparative studies, the mixed triple-decker complexes Eu2\[Pc(15C5)4](TPP)2 (2) and Eu2\[Pc(15C5)4]2(TPP) (3) were also synthesised by the raise-by-one-story method. These mixed ring sandwich complexes were characterised by various spectroscopic methods. Up to four one-electron oxidations and two one-electron reductions were revealed by cyclic voltammetry (CV) and differential pulse voltammetry (DPV). As shown by electronic absorption and infrared spectroscopy, supramolecular dimers (SM1 and SM3) were formed from the corresponding double-decker 1 and triple-decker 3 in the presence of potassium ions in MeOH/CHCl3.

Disorderly categories in picture postcards from colonial Papua and New Guinea

At the turn of the century in Melbourne, a notice typed on the verso of a postcard stated that the South Yarra Baptist Young Men's class was meeting on the following Sunday at 2.45 p.m. The card, published in the United Kingdom, was numbered 51828 in the Valentine series of Papuan postcards.1 The image, a photograph of Hanuabada village taken in the early 1880s, and the text, written early in 1900, are contradictory and constitute separate realms of evidence that invite a renegotiation of meaning, analysis, and interpretation of the relationships between images, tourism, colonial rule, and ethnographic knowing. The visual evidence suggests the postcard may have played an ethnographic, educative role in the public understanding of Papua, which had just become an Australian Territory and was not yet well known. It is also suggestive of educative roles related to mission endeavours, subimperialist ambitions and the new tourist traffic through the ports of Port Moresby, Samarai, and Rabaul.

A new low temperature synthesis route of fraipontite (Zn,Al)3(Si,Al)2O5(OH)4

A low temperature synthesis method based on the decomposition of urea at 90°C in water has been developed to synthesise fraipontite. This material is characterised by a basal reflection 001 at 7.44 Å. The trioctahedral nature of the fraipontite is shown by the presence of a 06l band around 1.54 Å, while a minor band around 1.51 Å indicates some cation ordering between Zn and Al resulting in Al-rich areas with a more dioctahedral nature. TEM and IR indicate that no separate kaolinite phase is present. An increase in the Al content however, did result in the formation of some SiO2 in the form of quartz. Minor impurities of carbonate salts were observed during the synthesis caused by to the formation of CO32- during the decomposition of urea.