The origin and evolution of phototropins.

Plant phototropism, the ability to bend toward or away from light, is predominantly controlled by blue-light photoreceptors, the phototropins. Although phototropins have been well-characterized in Arabidopsis thaliana, their evolutionary history is largely unknown. In this study, we complete an in-depth survey of phototropin homologs across land plants and algae using newly available transcriptomic and genomic data. We show that phototropins originated in an ancestor of Viridiplantae (land plants + green algae). Phototropins repeatedly underwent independent duplications in most major land-plant lineages (mosses, lycophytes, ferns, and seed plants), but remained single-copy genes in liverworts and hornworts-an evolutionary pattern shared with another family of photoreceptors, the phytochromes. Following each major duplication event, the phototropins differentiated in parallel, resulting in two specialized, yet partially overlapping, functional forms that primarily mediate either low- or high-light responses. Our detailed phylogeny enables us to not only uncover new phototropin lineages, but also link our understanding of phototropin function in Arabidopsis with what is known in Adiantum and Physcomitrella (the major model organisms outside of flowering plants). We propose that the convergent functional divergences of phototropin paralogs likely contributed to the success of plants through time in adapting to habitats with diverse and heterogeneous light conditions.

The Origin and Diversification of Birds.

Birds are one of the most recognizable and diverse groups of modern vertebrates. Over the past two decades, a wealth of new fossil discoveries and phylogenetic and macroevolutionary studies has transformed our understanding of how birds originated and became so successful. Birds evolved from theropod dinosaurs during the Jurassic (around 165-150 million years ago) and their classic small, lightweight, feathered, and winged body plan was pieced together gradually over tens of millions of years of evolution rather than in one burst of innovation. Early birds diversified throughout the Jurassic and Cretaceous, becoming capable fliers with supercharged growth rates, but were decimated at the end-Cretaceous extinction alongside their close dinosaurian relatives. After the mass extinction, modern birds (members of the avian crown group) explosively diversified, culminating in more than 10,000 species distributed worldwide today.

The empirical analysis of cigarette tax avoidance and illicit trade in Vietnam, 1998-2010.

Illicit trade carries the potential to magnify existing tobacco-related health care costs through increased availability of untaxed and inexpensive cigarettes. What is known with respect to the magnitude of illicit trade for Vietnam is produced primarily by the industry, and methodologies are typically opaque. Independent assessment of the illicit cigarette trade in Vietnam is vital to tobacco control policy. This paper measures the magnitude of illicit cigarette trade for Vietnam between 1998 and 2010 using two methods, discrepancies between legitimate domestic cigarette sales and domestic tobacco consumption estimated from surveys, and trade discrepancies as recorded by Vietnam and trade partners. The results indicate that Vietnam likely experienced net smuggling in during the period studied. With the inclusion of adjustments for survey respondent under-reporting, inward illicit trade likely occurred in three of the four years for which surveys were available. Discrepancies in trade records indicate that the value of smuggled cigarettes into Vietnam ranges from $100 million to $300 million between 2000 and 2010 and that these cigarettes primarily originate in Singapore, Hong Kong, Macao, Malaysia, and Australia. Notable differences in trends over time exist between the two methods, but by comparison, the industry estimates consistently place the magnitude of illicit trade at the upper bounds of what this study shows. The unavailability of annual, survey-based estimates of consumption may obscure the true, annual trend over time. Second, as surveys changed over time, estimates relying on them may be inconsistent with one another. Finally, these two methods measure different components of illicit trade, specifically consumption of illicit cigarettes regardless of origin and smuggling of cigarettes into a particular market. However, absent a gold standard, comparisons of different approaches to illicit trade measurement serve efforts to refine and improve measurement approaches and estimates.

Global Rates of Free Hydrogen (H2) Production by Serpentinization and other Abiogenic Processes within Young Ocean Crust

The main conclusion of this dissertation is that global H2 production within young ocean crust (<10 Mya) is higher than currently recognized, in part because current estimates of H2 production accompanying the serpentinization of peridotite may be too low (Chapter 2) and in part because a number of abiogenic H2-producing processes have heretofore gone unquantified (Chapter 3). The importance of free H2 to a range of geochemical processes makes the quantitative understanding of H2 production advanced in this dissertation pertinent to an array of open research questions across the geosciences (e.g. the origin and evolution of life and the oxidation of the Earth’s atmosphere and oceans).

The first component of this dissertation (Chapter 2) examines H2 produced within young ocean crust [e.g. near the mid-ocean ridge (MOR)] by serpentinization. In the presence of water, olivine-rich rocks (peridotites) undergo serpentinization (hydration) at temperatures of up to ~500°C but only produce H2 at temperatures up to ~350°C. A simple analytical model is presented that mechanistically ties the process to seafloor spreading and explicitly accounts for the importance of temperature in H2 formation. The model suggests that H2 production increases with the rate of seafloor spreading and the net thickness of serpentinized peridotite (S-P) in a column of lithosphere. The model is applied globally to the MOR using conservative estimates for the net thickness of lithospheric S-P, our least certain model input. Despite the large uncertainties surrounding the amount of serpentinized peridotite within oceanic crust, conservative model parameters suggest a magnitude of H2 production (~1012 moles H2/y) that is larger than the most widely cited previous estimates (~1011 although previous estimates range from 1010-1012 moles H2/y). Certain model relationships are also consistent with what has been established through field studies, for example that the highest H2 fluxes (moles H2/km2 seafloor) are produced near slower-spreading ridges (<20 mm/y). Other modeled relationships are new and represent testable predictions. Principal among these is that about half of the H2 produced globally is produced off-axis beneath faster-spreading seafloor (>20 mm/y), a region where only one measurement of H2 has been made thus far and is ripe for future investigation.

In the second part of this dissertation (Chapter 3), I construct the first budget for free H2 in young ocean crust that quantifies and compares all currently recognized H2 sources and H2 sinks. First global estimates of budget components are proposed in instances where previous estimate(s) could not be located provided that the literature on that specific budget component was not too sparse to do so. Results suggest that the nine known H2 sources, listed in order of quantitative importance, are: Crystallization (6x1012 moles H2/y or 61% of total H2 production), serpentinization (2x1012 moles H2/y or 21%), magmatic degassing (7x1011 moles H2/y or 7%), lava-seawater interaction (5x1011 moles H2/y or 5%), low-temperature alteration of basalt (5x1011 moles H2/y or 5%), high-temperature alteration of basalt (3x1010 moles H2/y or <1%), catalysis (3x108 moles H2/y or <<1%), radiolysis (2x108 moles H2/y or <<1%), and pyrite formation (3x106 moles H2/y or <<1%). Next we consider two well-known H2 sinks, H2 lost to the ocean and H2 occluded within rock minerals, and our analysis suggests that both are of similar size (both are 6x1011 moles H2/y). Budgeting results suggest a large difference between H2 sources (total production = 1x1013 moles H2/y) and H2 sinks (total losses = 1x1011 moles H2/y). Assuming this large difference represents H2 consumed by microbes (total consumption = 9x1011 moles H2/y), we explore rates of primary production by the chemosynthetic, sub-seafloor biosphere. Although the numbers presented require further examination and future modifications, the analysis suggests that the sub-seafloor H2 budget is similar to the sub-seafloor CH4 budget in the sense that globally significant quantities of both of these reduced gases are produced beneath the seafloor but never escape the seafloor due to microbial consumption.

The third and final component of this dissertation (Chapter 4) explores the self-organization of barchan sand dune fields. In nature, barchan dunes typically exist as members of larger dune fields that display striking, enigmatic structures that cannot be readily explained by examining the dynamics at the scale of single dunes, or by appealing to patterns in external forcing. To explore the possibility that observed structures emerge spontaneously as a collective result of many dunes interacting with each other, we built a numerical model that treats barchans as discrete entities that interact with one another according to simplified rules derived from theoretical and numerical work, and from field observations: Dunes exchange sand through the fluxes that leak from the downwind side of each dune and are captured on their upstream sides; when dunes become sufficiently large, small dunes are born on their downwind sides (“calving”); and when dunes collide directly enough, they merge. Results show that these relatively simple interactions provide potential explanations for a range of field-scale phenomena including isolated patches of dunes and heterogeneous arrangements of similarly sized dunes in denser fields. The results also suggest that (1) dune field characteristics depend on the sand flux fed into the upwind boundary, although (2) moving downwind, the system approaches a common attracting state in which the memory of the upwind conditions vanishes. This work supports the hypothesis that calving exerts a first order control on field-scale phenomena; it prevents individual dunes from growing without bound, as single-dune analyses suggest, and allows the formation of roughly realistic, persistent dune field patterns.

Phase Locked Loop and Modulo Games, The Dogma Loops; and “Finding Ibrida”

This dissertation consists of two independent musical compositions and an article detailing the process of the design and assembly of an electric guitar with particular emphasis on the carefully curated suite of embedded effects.

The first piece, 'Phase Locked Loop and Modulo Games' is scored for electric guitar and a single echo of equal volume less than a beat away. One could think of the piece as a 15 minute canon at the unison at the dotted eighth note (or at times the quarter or triplet-quarter), however the compositional motivation is more about weaving a composite texture between the guitar and its echo that is, while in theory extremely contrapuntal, in actuality is simply a single [superhuman] melodic line.

The second piece, 'The Dogma Loops' picks up a few compositional threads left by ‘Phase Locked Loop’ and weaves them into an entirely new tapestry. 'Phase Locked Loop' is motivated by the creation of a complex musical composite that is for the most part electronically transparent. 'The Dogma Loops' questions that same notion of composite electronic complexity by essentially asking a question: "what are the inputs to an interactive electronic system that create the most complex outputs via the simplest musical means possible?"

'The Dogma Loops' is scored for Electric Guitar (doubling on Ukulele), Violin and Violoncello. All of the principal instruments require an electronic pickup (except the Uke). The work is in three sections played attacca; [Automation Games], [Point of Origin] and [Cloning Vectors].

The third and final component of the document is the article 'Finding Ibrida.' This article details the process of the design and assembly of an electric guitar with integrated effects, while also providing the deeper context (conceptual and technical) which motivated the efforts and informed the challenges to hybridize the various technologies (tubes, transistors, digital effects and a microcontroller subsystem). The project was motivated by a desire for rigorous technical and hands-on engagement with analog signal processing as applied to the electric guitar. ‘Finding Ibrida’ explores sound, some myths and lore of guitar tech and the history of electric guitar distortion and its culture of sonic exploration.

Editor's choice Regional trade agreements and export competitiveness: the uncertain path of Nicaragua’s apparel exports under CAFTA

The Central American Free Trade Agreement (CAFTA) has been a mixed blessing for economic development. While exports to the US economy have increased, dependency may hinder economic growth if countries do not diversify or upgrade before temporary provisions expire. This article evaluates the impact of the temporary Tariff Preference Levels (TPLs) granted to Nicaragua under CAFTA and the consequences of TPL expiration. Using trade statistics, country- and firm-level data from Nicaragua’s National Free Zones Commission (CNZF) and data from field research, we estimate Nicaragua’s apparel sector will contract as much as 30–40% after TPLs expire. Our analysis underscores how rules of origin and firm nationality affect where and how companies do business, and in so doing, often constrain sustainable export growth.