ASU Scholarship Showcase

In this synthesis, we hope to accomplish two things: 1) reflect on how the analysis of the new archaeological cases presented in this special feature adds to previous case studies by revisiting a set of propositions reported in a 2006 special feature, and 2) reflect on four main ideas that are more specific to the archaeological cases: i) societal choices are influenced by robustness–vulnerability trade-offs, ii) there is interplay between robustness–vulnerability trade-offs and robustness–performance trade-offs, iii) societies often get locked in to particular strategies, and iv) multiple positive feedbacks escalate the perceived cost of societal change. We then discuss whether these lock-in traps can be prevented or whether the risks associated with them can be mitigated. We conclude by highlighting how these long-term historical studies can help us to understand current society, societal practices, and the nexus between ecology and society.

What relationships can be understood between resilience and vulnerability in social-ecological systems? In particular, what vulnerabilities are exacerbated or ameliorated by different sets of social practices associated with water management? These questions have been examined primarily through the study of contemporary or recent historic cases. Archaeology extends scientific observation beyond all social memory and can thus illuminate interactions occurring over centuries or millennia. We examined trade-offs of resilience and vulnerability in the changing social, technological, and environmental contexts of three long-term, pre-Hispanic sequences in the U.S. Southwest: the Mimbres area in southwestern New Mexico (AD 650–1450), the Zuni area in northern New Mexico (AD 850–1540), and the Hohokam area in central Arizona (AD 700–1450). In all three arid landscapes, people relied on agricultural systems that depended on physical and social infrastructure that diverted adequate water to agricultural soils. However, investments in infrastructure varied across the cases, as did local environmental conditions. Zuni farming employed a variety of small-scale water control strategies, including centuries of reliance on small runoff agricultural systems; Mimbres fields were primarily watered by small-scale canals feeding floodplain fields; and the Hohokam area had the largest canal system in pre-Hispanic North America. The cases also vary in their historical trajectories: at Zuni, population and resource use remained comparatively stable over centuries, extending into the historic period; in the Mimbres and Hohokam areas, there were major demographic and environmental transformations. Comparisons across these cases thus allow an understanding of factors that promote vulnerability and influence resilience in specific contexts.

Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to energy thus sustaining all higher life on Earth. Two large membrane protein complexes, photosystem I and II (PSI and PSII), act in series to catalyse the light-driven reactions in photosynthesis. PSII catalyses the light-driven water splitting process, which maintains the Earth’s oxygenic atmosphere. In this process, the oxygen-evolving complex (OEC) of PSII cycles through five states, S₀ to S₄, in which four electrons are sequentially extracted from the OEC in four light-driven charge-separation events. Here we describe time resolved experiments on PSII nano/microcrystals from Thermosynechococcus elongatus performed with the recently developed technique of serial femtosecond crystallography. Structures have been determined from PSII in the dark S₁ state and after double laser excitation (putative S₃ state) at 5 and 5.5 Å resolution, respectively. The results provide evidence that PSII undergoes significant conformational changes at the electron acceptor side and at the Mn₄CaO₅ core of the OEC. These include an elongation of the metal cluster, accompanied by changes in the protein environment, which could allow for binding of the second substrate water molecule between the more distant protruding Mn (referred to as the ‘dangler’ Mn) and the Mn₃CaO_x cubane in the S₂ to S₃ transition, as predicted by spectroscopic and computational studies. This work shows the great potential for time-resolved serial femtosecond crystallography for investigation of catalytic processes in biomolecules.

We present results from experiments at the Linac Coherent Light Source (LCLS) demonstrating that serial femtosecond crystallography (SFX) can be performed to high resolution (~2.5 Å) using protein microcrystals deposited on an ultra-thin silicon nitride membrane and embedded in a preservation medium at room temperature. Data can be acquired at a high acquisition rate using x-ray free electron laser sources to overcome radiation damage, while sample consumption is dramatically reduced compared to flowing jet methods. We achieved a peak data acquisition rate of 10 Hz with a hit rate of ~38%, indicating that a complete data set could be acquired in about one 12-hour LCLS shift using the setup described here, or in even less time using hardware optimized for fixed target SFX. This demonstration opens the door to ultra low sample consumption SFX using the technique of diffraction-before-destruction on proteins that exist in only small quantities and/or do not produce the copious quantities of microcrystals required for flowing jet methods.

Previous proof-of-concept measurements on single-layer two-dimensional membrane-protein crystals performed at X-ray free-electron lasers (FELs) have demonstrated that the collection of meaningful diffraction patterns, which is not possible at synchrotrons because of radiation-damage issues, is feasible. Here, the results obtained from the analysis of a thousand single-shot, room-temperature X-ray FEL diffraction images from two-dimensional crystals of a bacteriorhodopsin mutant are reported in detail. The high redundancy in the measurements boosts the intensity signal-to-noise ratio, so that the values of the diffracted intensities can be reliably determined down to the detector-edge resolution of 4 Å. The results show that two-dimensional serial crystallography at X-ray FELs is a suitable method to study membrane proteins to near-atomic length scales at ambient temperature. The method presented here can be extended to pump–probe studies of optically triggered structural changes on submillisecond timescales in two-dimensional crystals, which allow functionally relevant large-scale motions that may be quenched in three-dimensional crystals.

The insights in Governing the Commons have provided foundational ideas for commons research in the past 23 years. However, the cases that Elinor Ostrom analyzed have been exposed to new social, economic, and ecological disturbances. What has happened to these cases since the 1980s? We reevaluated one of Ostrom’s case studies, the lobster and groundfishery of Port Lameron, Southwest Nova Scotia (SWNS). Ostrom suggested that the self-governance of this fishery was fragile because the government did not recognize the rights of resource users to organize their own rules. In the Maine lobster fishery, however, the government formalized customary rules and decentralized power to fishing ports. We applied the concepts of feedback, governance mismatches, and the robustness of social-ecological systems to understand the pathway of institutional change in Port Lameron. We revisited the case of Port Lameron using marine harvesters’ accounts collected from participant observation, informal interviews and surveys, and literature on fisheries policy and ecology in SWNS and Maine. We found that the government’s failure to recognize the customary rights of harvesters to organize has weakened feedback between the operational level, where resource users interact with the resource, and the collective-choice level, where agents develop rules to influence the behavior of resource users. This has precipitated governance mismatches, which have led harvesters to believe that the decision-making process is detrimental to their livelihoods. Thus, harvesters rarely participate in decision making and resist regulatory change. In Maine, harvesters can influence decisions through participation, but there is a trade-off. With higher influence in decisions, captains have co-opted the decision-making process. Nevertheless, we suggest that the fisheries of SWNS are more vulnerable to social-ecological change because of weaker feedbacks than in Maine. Finally, we have discussed the potential benefits of polycentricity to both fisheries.

We describe the deposition of four datasets consisting of X-ray diffraction images acquired using serial femtosecond crystallography experiments on microcrystals of human G protein-coupled receptors, grown and delivered in lipidic cubic phase, at the Linac Coherent Light Source. The receptors are: the human serotonin receptor 2B in complex with an agonist ergotamine, the human δ-opioid receptor in complex with a bi-functional peptide ligand DIPP-NH₂, the human smoothened receptor in complex with an antagonist cyclopamine, and finally the human angiotensin II type 1 receptor in complex with the selective antagonist ZD7155. All four datasets have been deposited, with minimal processing, in an HDF5-based file format, which can be used directly for crystallographic processing with CrystFEL or other software. We have provided processing scripts and supporting files for recent versions of CrystFEL, which can be used to validate the data.

The planetary boundary framework constitutes an opportunity for decision makers to define climate policy through the lens of adaptive governance. Here, we use the DICE model to analyze the set of adaptive climate policies that comply with the two planetary boundaries related to climate change: (1) staying below a CO₂ concentration of 550 ppm until 2100 and (2) returning to 350 ppm in 2100. Our results enable decision makers to assess the following milestones: (1) a minimum of 33% reduction of CO₂ emissions by 2055 in order to stay below 550 ppm by 2100 (this milestone goes up to 46% in the case of delayed policies); and (2) carbon neutrality and the effective implementation of innovative geoengineering technologies (10% negative emissions) before 2060 in order to return to 350 ppm in 2100, under the assumption of getting out of the baseline scenario without delay. Finally, we emphasize the need to use adaptive path-based approach instead of single point target for climate policy design.

Structural studies on living cells by conventional methods are limited to low resolution because radiation damage kills cells long before the necessary dose for high resolution can be delivered. X-ray free-electron lasers circumvent this problem by outrunning key damage processes with an ultra-short and extremely bright coherent X-ray pulse. Diffraction-before-destruction experiments provide high-resolution data from cells that are alive when the femtosecond X-ray pulse traverses the sample. This paper presents two data sets from micron-sized cyanobacteria obtained at the Linac Coherent Light Source, containing a total of 199,000 diffraction patterns. Utilizing this type of diffraction data will require the development of new analysis methods and algorithms for studying structure and structural variability in large populations of cells and to create abstract models. Such studies will allow us to understand living cells and populations of cells in new ways. New X-ray lasers, like the European XFEL, will produce billions of pulses per day, and could open new areas in structural sciences.

The context in which many self-governed commons systems operate will likely be significantly altered as globalization processes play out over the next few decades. Such dramatic changes will induce some systems to fail and subsequently to be transformed, rather than merely adapt. Despite this possibility, research on globalization-induced transformations of social-ecological systems (SESs) is still underdeveloped. We seek to help fill this gap by exploring some patterns of transformation in SESs and the question of what factors help explain the persistence of cooperation in the use of common-pool resources through transformative change. Through the analysis of 89 forest commons in South Korea that experienced such transformations, we found that there are two broad types of transformation, cooperative and noncooperative. We also found that two system-level properties, transaction costs associated group size and network diversity, may affect the direction of transformation. SESs with smaller group sizes and higher network diversity may better organize cooperative transformations when the existing system becomes untenable.