Constraints on the carbon cycle and climate during the early evolution of animals

One of the greatest challenges in science lies in disentangling causality in complex, coupled systems. This is illustrated no better than in the dynamic interplay between the Earth and life. The early evolution and diversification of animals occurred within a backdrop of global change, yet reconstructing the potential role of the environment in this evolutionary transition is challenging. In the 200 million years from the end-Cryogenian to the Ordovician, enigmatic Ediacaran fauna explored body plans, animals diversified and began to biomineralize, forever changing the ocean's chemical cycles, and the biological community in shallow marine ecosystems transitioned from a microbial one to an animal one.

In the following dissertation, a multi-faceted approach combining macro- and micro-scale analyses is presented that draws on the sedimentology, geochemistry and paleontology of the rocks that span this transition to better constrain the potential environmental changes during this interval.

In Chapter 1, the potential of clumped isotope thermometry in deep time is explored by assessing the importance of burial and diagenesis on the thermometer. Eocene- to Precambrian-aged carbonates from the Sultanate of Oman were analyzed from current burial depths of 350-5850 meters. Two end-member styles of diagenesis independent of burial depth were observed.

Chapters 2, 3 and 4 explore the fallibility of the Ediacaran carbon isotope record and aspects of the sedimentology and geochemistry of the rocks preserving the largest negative carbon isotope excursion on record---the Shuram Excursion. Chapter 2 documents the importance of temperature, fluid composition and mineralogy on the delta 18-O min record and interrogates the bulk trace metal signal. Chapter 3 explores the spatial variability in delta 13-C recorded in the transgressive Johnnie Oolite and finds a north-to-south trend recording the onset of the excursion. Chapter 4 investigates the nature of seafloor precipitation during this excursion and more broadly. We document the potential importance of microbial respiratory reactions on the carbonate chemistry of the sediment-water interface through time.

Chapter 5 investigates the latest Precambrian sedimentary record in carbonates from the Sultanate of Oman, including how delta 13-C and delta 34-S CAS vary across depositional and depth gradients. A new model for the correlation of the Buah and Ara formations across Oman is presented. Isotopic results indicate delta 13-C varies with relative eustatic change and delta 34-S CAS may vary in absolute magnitude across Oman.

Chapter 6 investigates the secular rise in delta 18-Omin in the early Paleozoic by using clumped isotope geochemistry on calcitic and phosphatic fossils from the Cambrian and Ordovician. Results do not indicate extreme delta 18-O seawater depletion and instead suggest warmer equatorial temperatures across the early Paleozoic.

Robust Control of Evolutionary Dynamics

The application of principles from evolutionary biology has long been used to gain new insights into the progression and clinical control of both infectious diseases and neoplasms. This iterative evolutionary process consists of expansion, diversification and selection within an adaptive landscape - species are subject to random genetic or epigenetic alterations that result in variations; genetic information is inherited through asexual reproduction and strong selective pressures such as therapeutic intervention can lead to the adaptation and expansion of resistant variants. These principles lie at the center of modern evolutionary synthesis and constitute the primary reasons for the development of resistance and therapeutic failure, but also provide a framework that allows for more effective control.

A model system for studying the evolution of resistance and control of therapeutic failure is the treatment of chronic HIV-1 infection by broadly neutralizing antibody (bNAb) therapy. A relatively recent discovery is that a minority of HIV-infected individuals can produce broadly neutralizing antibodies, that is, antibodies that inhibit infection by many strains of HIV. Passive transfer of human antibodies for the prevention and treatment of HIV-1 infection is increasingly being considered as an alternative to a conventional vaccine. However, recent evolution studies have uncovered that antibody treatment can exert selective pressure on virus that results in the rapid evolution of resistance. In certain cases, complete resistance to an antibody is conferred with a single amino acid substitution on the viral envelope of HIV.

The challenges in uncovering resistance mechanisms and designing effective combination strategies to control evolutionary processes and prevent therapeutic failure apply more broadly. We are motivated by two questions: Can we predict the evolution to resistance by characterizing genetic alterations that contribute to modified phenotypic fitness? Given an evolutionary landscape and a set of candidate therapies, can we computationally synthesize treatment strategies that control evolution to resistance?

To address the first question, we propose a mathematical framework to reason about evolutionary dynamics of HIV from computationally derived Gibbs energy fitness landscapes -- expanding the theoretical concept of an evolutionary landscape originally conceived by Sewall Wright to a computable, quantifiable, multidimensional, structurally defined fitness surface upon which to study complex HIV evolutionary outcomes.

To design combination treatment strategies that control evolution to resistance, we propose a methodology that solves for optimal combinations and concentrations of candidate therapies, and allows for the ability to quantifiably explore tradeoffs in treatment design, such as limiting the number of candidate therapies in the combination, dosage constraints and robustness to error. Our algorithm is based on the application of recent results in optimal control to an HIV evolutionary dynamics model and is constructed from experimentally derived antibody resistant phenotypes and their single antibody pharmacodynamics. This method represents a first step towards integrating principled engineering techniques with an experimentally based mathematical model in the rational design of combination treatment strategies and offers predictive understanding of the effects of combination therapies of evolutionary dynamics and resistance of HIV. Preliminary in vitro studies suggest that the combination antibody therapies predicted by our algorithm can neutralize heterogeneous viral populations despite containing resistant mutations.

Studies of Zγ production and constraints on anomalous triple gauge couplings in pp collisions at √s = 7 TeV

In this thesis, we test the electroweak sector of the Standard Model of particle physics through the measurements of the cross section of the simultaneous production of the neutral weak boson Z and photon γ, and the limits on the anomalous Zγγ and ZZγ triple gauge couplings h3 and h4 with the Z decaying to leptons (electrons and muons). We analyze events collected in proton-proton collisions at center of mass energy of sqrt(s) = 7 TeV corresponding to an integrated luminosity of 5.0 inverse femtobarn. The analyzed events were recorded by the Compact Muon Solenoid detector at the Large Hadron Collider in 2011.

The production cross section has been measured for hard photons with transverse momentum greater than 15 GeV that are separated from the the final state leptons in the eta-phi plane by Delta R greater than 0.7, whose sum of the transverse energy of hadrons over the transverse energy of the photon in a cone around the photon with Delta R less than 0.3 is less than 0.5, and with the invariant mass of the dilepton system greater than 50 GeV. The measured cross section value is 5.33 +/- 0.08 (stat.) +/- 0.25 (syst.) +/- 0.12 (lumi.) picobarn. This is compatible with the Standard Model prediction that includes next-to-leading-order QCD contributions: 5.45 +/- 0.27 picobarn.

The measured 95 % confidence-level upper limits on the absolute values of the anomalous couplings h3 and h4 are 0.01 and 8.8E-5 for the Zγγ interactions, and, 8.6E-3 and 8.0E-5 for the ZZγ interactions. These values are also compatible with the Standard Model where they vanish in the tree-level approximation. They extend the sensitivity of the 2012 results from the ATLAS collaboration based on 1.02 inverse femtobarn of data by a factor of 2.4 to 3.1.

Limits and tradeoffs in the control of autocatalytic systems

Despite the complexity of biological networks, we find that certain common architectures govern network structures. These architectures impose fundamental constraints on system performance and create tradeoffs that the system must balance in the face of uncertainty in the environment. This means that while a system may be optimized for a specific function through evolution, the optimal achievable state must follow these constraints. One such constraining architecture is autocatalysis, as seen in many biological networks including glycolysis and ribosomal protein synthesis. Using a minimal model, we show that ATP autocatalysis in glycolysis imposes stability and performance constraints and that the experimentally well-studied glycolytic oscillations are in fact a consequence of a tradeoff between error minimization and stability. We also show that additional complexity in the network results in increased robustness. Ribosome synthesis is also autocatalytic where ribosomes must be used to make more ribosomal proteins. When ribosomes have higher protein content, the autocatalysis is increased. We show that this autocatalysis destabilizes the system, slows down response, and also constrains the system’s performance. On a larger scale, transcriptional regulation of whole organisms also follows architectural constraints and this can be seen in the differences between bacterial and yeast transcription networks. We show that the degree distributions of bacterial transcription network follow a power law distribution while the yeast network follows an exponential distribution. We then explored the evolutionary models that have previously been proposed and show that neither the preferential linking model nor the duplication-divergence model of network evolution generates the power-law, hierarchical structure found in bacteria. However, in real biological systems, the generation of new nodes occurs through both duplication and horizontal gene transfers, and we show that a biologically reasonable combination of the two mechanisms generates the desired network.

Plate tectonic constraints on flat subduction and paleomagnetic constraints on rifting

Plate tectonics shapes our dynamic planet through the creation and destruction of lithosphere. This work focuses on increasing our understanding of the processes at convergent and divergent boundaries through geologic and geophysical observations at modern plate boundaries. Recent work had shown that the subducting slab in central Mexico is most likely the flattest on Earth, yet there was no consensus about what caused it to originate. The first chapter of this thesis sets out to systematically test all previously proposed mechanisms for slab flattening on the Mexican case. What we have discovered is that there is only one model for which we can find no contradictory evidence. The lack of applicability of the standard mechanisms used to explain flat subduction in the Mexican example led us to question their applications globally. The second chapter expands the search for a cause of flat subduction, in both space and time. We focus on the historical record of flat slabs in South America and look for a correlation between the shallowing and steepening of slab segments with relation to the inferred thickness of the subducting oceanic crust. Using plate reconstructions and the assumption that a crustal anomaly formed on a spreading ridge will produce two conjugate features, we recreate the history of subduction along the South American margin and find that there is no correlation between the subduction of a bathymetric highs and shallow subduction. These studies have proven that a subducting crustal anomaly is neither a sufficient or necessary condition of flat slab subduction. The final chapter in this thesis looks at the divergent plate boundary in the Gulf of California. Through geologic reconnaissance mapping and an intensive paleomagnetic sampling campaign, we try to constrain the location and orientation of a widespread volcanic marker unit, the Tuff of San Felipe. Although the resolution of the applied magnetic susceptibility technique proved inadequate to contain the direction of the pyroclastic flow with high precision, we have been able to detect the tectonic rotation of coherent blocks as well as rotation within blocks.

Essays in optimal resource allocation under uncertainty with capacity constraints

This thesis brings together four papers on optimal resource allocation under uncertainty with capacity constraints. The first is an extension of the Arrow-Debreu contingent claim model to a good subject to supply uncertainty for which delivery capacity has to be chosen before the uncertainty is resolved. The second compares an ex-ante contingent claims market to a dynamic market in which capacity is chosen ex-ante and output and consumption decisions are made ex-post. The third extends the analysis to a storable good subject to random supply. Finally, the fourth examines optimal allocation of water under an appropriative rights system.

Structural and clumped-isotope constraints on the mechanisms of displacement along low-angle detachments

Despite years of research on low-angle detachments, much about them remains enigmatic. This thesis addresses some of the uncertainty regarding two particular detachments, the Mormon Peak detachment in Nevada and the Heart Mountain detachment in Wyoming and Montana.

Constraints on the geometry and kinematics of emplacement of the Mormon Peak detachment are provided by detailed geologic mapping of the Meadow Valley Mountains, along with an analysis of structural data within the allochthon in the Mormon Mountains. Identifiable structures well suited to constrain the kinematics of the detachment include a newly mapped, Sevier-age monoclinal flexure in the hanging wall of the detachment. This flexure, including the syncline at its base and the anticline at its top, can be readily matched to the base and top of the frontal Sevier thrust ramp, which is exposed in the footwall of the detachment to the east in the Mormon Mountains and Tule Springs Hills. The ~12 km of offset of these structural markers precludes the radial sliding hypothesis for emplacement of the allochthon.

The role of fluids in the slip along faults is a widely investigated topic, but the use of carbonate clumped-isotope thermometry to investigate these fluids is new. Faults rocks from within ~1 m of the Mormon Peak detachment, including veins, breccias, gouges, and host rocks, were analyzed for carbon, oxygen, and clumped-isotope measurements. The data indicate that much of the carbonate breccia and gouge material along the detachment is comminuted host rock, as expected. Measurements in vein material indicate that the fluid system is dominated by meteoric water, whose temperature indicates circulation to substantial depths (c. 4 km) in the upper crust near the fault zone.

Slip along the subhorizontal Heart Mountain detachment is particularly enigmatic, and many different mechanisms for failure have been proposed, predominantly involving catastrophic failure. Textural evidence of multiple slip events is abundant, and include multiple brecciation events and cross-cutting clastic dikes. Footwall deformation is observed in numerous exposures of the detachment. Stylolitic surfaces and alteration textures within and around “banded grains” previously interpreted to be an indicator of high-temperature fluidization along the fault suggest their formation instead via low-temperature dissolution and alteration processes. There is abundant textural evidence of the significant role of fluids along the detachment via pressure solution. The process of pressure solution creep may be responsible for enabling multiple slip events on the low-angle detachment, via a local rotation of the stress field.

Clumped-isotope thermometry of fault rocks associated with the Heart Mountain detachment indicates that despite its location on the flanks of a volcano that was active during slip, the majority of carbonate along the Heart Mountain detachment does not record significant heating above ambient temperatures (c. 40-70°C). Instead, cold meteoric fluids infiltrated the detachment breccia, and carbonate precipitated under ambient temperatures controlled by structural depth. Locally, fault gouge does preserve hot temperatures (>200°C), as is observed in both the Mormon Peak detachment and Heart Mountain detachment areas. Samples with very hot temperatures attributable to frictional shear heating are present but rare. They appear to be best preserved in hanging wall structures related to the detachment, rather than along the main detachment.

Evidence is presented for the prevalence of relatively cold, meteoric fluids along both shallow crustal detachments studied, and for protracted histories of slip along both detachments. Frictional heating is evident from both areas, but is a minor component of the preserved fault rock record. Pressure solution is evident, and might play a role in initiating slip on the Heart Mountain fault, and possibly other low-angle detachments.

Manganese: Minerals, Microbes, and the Evolution of Oxygenic Photosynthesis

Oxygenic photosynthesis fundamentally transformed our planet by releasing molecular oxygen and altering major biogeochemical cycles, and this exceptional metabolism relies on a redox-active cubane cluster of four manganese atoms. Not only is manganese essential for producing oxygen, but manganese is also only oxidized by oxygen and oxygen-derived species. Thus the history of manganese oxidation provides a valuable perspective on our planet’s environmental past, the ancient availability of oxygen, and the evolution of oxygenic photosynthesis. Broadly, the general trends of the geologic record of manganese deposition is a chronicle of ancient manganese oxidation: manganese is introduced into the fluid Earth as Mn(II) and it will remain only a trace component in sedimentary rocks until it is oxidized, forming Mn(III,IV) insoluble precipitates that are concentrated in the rock record. Because these manganese oxides are highly favorable electron acceptors, they often undergo reduction in sediments through anaerobic respiration and abiotic reaction pathways.

The following dissertation presents five chapters investigating manganese cycling both by examining ancient examples of manganese enrichments in the geologic record and exploring the mineralogical products of various pathways of manganese oxide reduction that may occur in sediments. The first chapter explores the mineralogical record of manganese and reports abundant manganese reduction recorded in six representative manganese-enriched sedimentary sequences. This is followed by a second chapter that further analyzes the earliest significant manganese deposit 2.4 billon years ago, and determines that it predated the origin of oxygenic photosynthesis and thus is supporting evidence for manganese-oxidizing photosynthesis as an evolutionary precursor prior to oxygenic photosynthesis. The lack of oxygen during this early manganese deposition was partially established using oxygen-sensitive detrital grains, and so a third chapter delves into what these grains mean for oxygen constraints using a mathematical model. The fourth chapter returns to processes affecting manganese post-deposition, and explores the relationships between manganese mineral products and (bio)geochemical reduction processes to understand how various manganese minerals can reveal ancient environmental conditions and biological metabolisms. Finally, a fifth chapter considers whether manganese can be mobilized and enriched in sedimentary rocks and determines that manganese was concentrated secondarily in a 2.5 billion-year-old example from South Africa. Overall, this thesis demonstrates how microbial processes, namely photosynthesis and metal oxide-reducing metabolisms, are linked to and recorded in the rich complexity of the manganese mineralogical record.

Volatiles in Protoplanetary Disks

Planets are assembled from the gas, dust, and ice in the accretion disks that encircle young stars. Ices of chemical compounds with low condensation temperatures (<200 K), the so-called volatiles, dominate the solid mass reservoir from which planetesimals are formed and are thus available to build the protoplanetary cores of gas/ice giant planets. It has long been thought that the regions near the condensation fronts of volatiles are preferential birth sites of planets. Moreover, the main volatiles in disks are also the main C-and O-containing species in (exo)planetary atmospheres. Understanding the distribution of volatiles in disks and their role in planet-formation processes is therefore of great interest.

This thesis addresses two fundamental questions concerning the nature of volatiles in planet-forming disks: (1) how are volatiles distributed throughout a disk, and (2) how can we use volatiles to probe planet-forming processes in disks? We tackle the first question in two complementary ways. We have developed a novel super-resolution method to constrain the radial distribution of volatiles throughout a disk by combining multi-wavelength spectra. Thanks to the ordered velocity and temperature profiles in disks, we find that detailed constraints can be derived even with spatially and spectrally unresolved data -- provided a wide range of energy levels are sampled. We also employ high-spatial resolution interferometric images at (sub)mm frequencies using the Atacama Large Millimeter Array (ALMA) to directly measure the radial distribution of volatiles.

For the second question, we combine volatile gas emission measurements with those of the dust continuum emission or extinction to understand dust growth mechanisms in disks and disk instabilities at planet-forming distances from the central star. Our observations and models support the idea that the water vapor can be concentrated in regions near its condensation front at certain evolutionary stages in the lifetime of protoplanetary disks, and that fast pebble growth is likely to occur near the condensation fronts of various volatile species.