Combinatorial effects on clumped isotopes and their significance in biogeochemistry

A new paper from Laurence Yeung on the fundamentals of “clumped-isotope” fractionation, was recently accepted in Geochimica et Cosmochimica Acta. It shows, through simple theoretical arguments, the factors influencing the occurrence of rare-isotope pairs in molecules when they are made. One might be able to base future tracers of biogeochemistry on these principles.

One of the findings is also a convenient practical summary: When playing Craps, never bet on snake eyes if you suspect the dice are loaded―it, along with the other hard rolls (double threes, double fours, etc.) are less likely to come up when the dice are not evenly weighted.

doi: 10.1016/j.gca.2015.09.020


The arrangement of isotopes within a collection of molecules records their physical and chemical histories. Clumped-isotope analysis interrogates these arrangements, i.e., how often rare isotopes are bound together, which in many cases can be explained by equilibrium and/or kinetic isotope fractionation. However, purely combinatorial effects, rooted in the statistics of pairing atoms in a closed system, are also relevant, and not well understood. Here, I show that combinatorial isotope effects are most important when two identical atoms are neighbors on the same molecule (e.g., O2, N2, and D-D clumping in CH4). When the two halves of an atom pair are either assembled with different isotopic preferences or drawn from different reservoirs, combinatorial effects cause depletions in clumped-isotope abundance that are most likely between zero and –1‰, although they could potentially be –10‰ or larger for D-D pairs. These depletions are of similar magnitude, but of opposite sign, to low-temperature equilibrium clumped-isotope effects for many small molecules. Enzymatic isotope-pairing reactions, which can have site-specific isotopic fractionation factors and atom reservoirs, should express this class of combinatorial isotope effect, although it is not limited to biological reactions. Chemical-kinetic isotope effects, which are related to a bond-forming transition state, arise independently and express second-order combinatorial effects related to the abundance of the rare isotope. Heteronuclear moeties (e.g., C–O and C–H), are insensitive to direct combinatorial influences, but secondary combinatorial influences are evident.

In general, both combinatorial and chemical-kinetic factors are important for calculating and interpreting clumped-isotope signatures of kinetically controlled reactions. I apply this analytical framework to isotope-pairing reactions relevant to geochemical oxygen, carbon, and nitrogen cycling that may be influenced by combinatorial clumped-isotope effects. These isotopic signatures, manifest as either directly bound isotope “clumps” or as features of a molecule’s isotopic anatomy, are linked to molecular mechanisms and may eventually provide additional information about biogeochemical cycling on environmentally relevant spatial scales.

Read more about the research in the Yeung Lab at

Mixed Carbonate–Siliciclastic Sedimentation Along the Great Barrier Reef Upper Slope: A Challenge to the Reciprocal Sedimentation Model



Journal of Sedimentary Research, 85: 1019–1036, 2015.

ABSTRACT: Results of studies involving numerous cores and ODP holes along the Great Barrier Reef (GBR) margin and adjacent Queensland Trough and Queensland Plateau have challenged the use of a reciprocal sedimentation model to describe the sedimentary response of slope and basin settings to glacioeustatic sea-level fluctuations. Upper-slope sedimentation results from the relationships between sea-level fluctuations, antecedent topography, and regional climate that play an important role in the type and amount of sediment deposited on the upper slope during glacial, deglacial, and interglacial times. During the Last Glacial Maximum (LGM, . 20 ka ago) upper-slope sediments generally lacked siliciclastic material and are characterized by very low accumulation rates, whereas early deglacial-time (Termination I, TI) deposits are dominated by a siliciclastic and neritic carbonate pulse. Siliciclastic sedimentation was significantly reduced in the Holocene, while carbonate sedimentation remains elevated. A new borehole, IODP Expedition 325 Hole M0058A (Hole 58A), recovered 82% of a 40.4 m hole on the upper slope east of Noggin Passage on the central GBR margin near Cairns, Australia. Hole 58A provides a detailed sedimentary record during Termination II (TII), Marine Isotope Stage 6/5e (MIS-6/5e), deglacial transition, and through most of interglacial MIS-5. This hole, along with two others (ODP Leg 133 Holes 820A and 819A from the upper slope east of Grafton Passage), show carbonate–siliciclastic cyclicity as the result of glacioeustatic change with the GBR shelf. Sedimentation at Hole 58A is consistent with that of previous studies along the GBR margin (focusing on the LGM to present), and extends the upper-slope sedimentary record back to TII and interglacial MIS-5. A siliciclastic pulse similar to the one during TI occurred during the penultimate deglaciation, TII; however, the maximum neritic aragonite export to the upper slope occurred not during peak MIS-5e highstand when sea level was a few meters above modern position, but subsequently during a time (MIS-5d to 5a) when lowered sea level fluctuated between 30 and 50 m below present sea level. Siliciclastic sediments were reworked and exported to the upper slope when the lowstand fluvial plain was re-flooded, whereas neritic carbonate export to the slope reached a maximum when sea level fell and much of the mid to outer shelf re-entered the photic zone, subsequent to a drowning interval. Thus, this analysis refines the mixed-sedimentation models of upper-slope sedimentation along the central GBR margin during the penultimate deglacial transgression and subsequent interglacial early and late highstand. This study provides further evidence that mixed carbonate–siliciclastic margins do not always behave in a predictable manner and that mixed margins both modern and ancient would benefit from detailed study of sediment transport in the context of sea-level rise and fall.

The onset of the Early Eocene Climatic Optimum at Branch Stream, Clarence River valley, New Zealand

The onset of the Early Eocene Climatic Optimum at Branch Stream, Clarence River valley, New Zealand

BS Slotnick, GR Dickens, CJ Hollis, JS Crampton, C Percy Strong & Andy Phillips (2015)

New Zealand Journal of Geology and Geophysics, DOI: 10.1080/00288306.2015.1063514

Abstract. We present new lithologic, biostratigraphic and carbon isotope records for a calcareous-rich ∼84m thick, early Eocene, upper continental slope section now exposed along Branch Stream, Marlborough. Decimetre-scale limestone-marl couplets comprise the section. Several marl-rich intervals correspond to carbon isotope excursions (CIEs) representing increased 13C -depleted carbon fluxes to the ocean. These records are similar to  those at nearby Mead Stream, except marl-rich intervals at Branch Stream are thicker with a wider δ13C range. Comparison to other sites indicates the section spans ∼53.4–51.6 Ma, the onset of the Early Eocene Climatic Optimum (EECO). The most prominent CIE is correlated with the K/X event (52.9 Ma). Prominent marl-rich intervals resulted from increased fluxes of terrigenous material and associated carbonate dilution. We find multiple warming events marked lowermost EECO, each probably signaling enhanced seasonal precipitation. Branch Stream bulk isotopic records suggest ’differential diagenesis’ impacted the sequence during sediment burial.

Keywords: Carbon isotope stratigraphy; Clarence Valley; Early Eocene Climatic Optimum; Eocene hyperthermals; global carbon cycling

An Experimental Study of Trace Element Fluxes from Subducted Oceanic Crust

New publication in Journal of Petrology from Laura Carter’s Master’s research at the University of Bristol with Susanne Skora, Jon Blundy, Tim Elliott, and Cees-Jan De Hoog at the University of Edinburgh. Carter et al. 2015

We have determined experimentally the hydrous phase relations and trace element partitioning behaviour of ocean floor basalt protoliths at pressures and temperatures (3 GPa, 750–1000C) relevant to melting in subduction zones. To avoid potential complexities associated with trace element doping of starting materials we have used natural, pristine mid-ocean ridge basalt (MORB from Kolbeinsey Ridge) and altered oceanic crust (AOC from Deep Sea Drilling Project leg 46, 20N Atlantic).  Approximately 15 wt % water was added to starting materials to simulate fluid fluxing from dehydrating serpentinite underlying the oceanic crust. The vapour-saturated solidus is sensitive to basalt K2O content, decreasing from 825 +/- 25C in MORB (0.04 wt % K2O) to 750C in AOC (0.25 wt % K2O). Textural evidence indicates that near-solidus fluids are sub-critical in nature. The residual solid assemblage in both MORB and AOC experiments is dominated by garnet and clinopyroxene, with accessory kyanite, epidote, Fe–Ti oxide and rutile (plus quartz–coesite, phengite and apatite below the solidus). Trace element analyses of quenched silica-rich melts show a strong temperature dependence of key trace elements. In contrast to the trace elementdoped starting materials of previous studies, we do not observe residual allanite. Instead, abundant residual epidote provides the host for thorium and light rare earth elements (LREE), preventing LREE from being released (RLREE <3ppm at 750–900C). Elevated Ba/Th ratios, characteristic of many arc basalts, are found to be generated within a narrow temperature field above the breakdown temperature of phengite, but below exhaustion of epidote. Melts with Ba/Th >1500 and La/SmPUM (where PUM indicates primitive upper mantle) 1, most closely matching the geochemical signal of arc lavas worldwide, were generated from AOC at 800–850C.


Geochemistry and thermodynamics of an earthquake: A case study of pseudotachylites within mylonitic granitoid

Insight to the enigmatic origin of the Hangai Dome in central Mongolia

Screen shot 2015-08-28 at 4.04.14 PMThe Hangai Dome in central Mongolia is one of the most bizarre high-elevation places in continental interiors on Earth. The Indian plate collides with the Eurasian plate to its southwest and the Pacific plate subducts under the Eurasian plate to its east. However, the Hangai Dome is very far (thousands of kilometers) away from the plate margin of East Asia where the tectonic plates converge. There have been debates on mechanisms that caused the uplift of Hangai Dome, whether it’s driven by the movement of tectonic plates or caused by the hot mantle rock rising from the deeper interior of the Earth. The new study by Chen et al. (2015, GRL) shows a clearly imaged localized deep mantle upwelling that generated magma in the rigid shell of the Earth (movie). The heat released by the magma makes the lithosphere underlying the dome more buoyant that caused the surface uplift of the dome. This unique example of continental uplift shows that the active mantle also plays an important role in shaping the Earth’s landscape and consequently the ecological habitat. For more detailed information on seismic adjoint tomography technique and data used in constructing the 3-D seismic model, please check out a different article by Chen et al. (2015, JGR) published earlier this year.

Laura carter

Hydrous basalt–limestone interaction at crustal conditions: Implications for generation of ultracalcic melts and outflux of CO2 at volcanic arcs

New student paper out!  See Laura Carter’s paper on basalt-limestone interactions with implications for arc CO2 fluxes, published in Earth and Planetary Science Letters. [article]


High degassing rates for some volcanoes, typically in continental arcs, (e.g., Colli Albani Volcanic District, Etna, Vesuvius, Italy; Merapi, Indonesia; Popocatepetl, Mexico) are thought to be influenced by magma–carbonate interaction in the crust. In order to constrain the nature of reaction and extent of carbonate breakdown, we simulated basalt–limestone wall-rock interactions at 0.5–1.0 GPa, 1100–1200 °C using a piston cylinder and equal mass fractions of calcite (CaCO3) and a hydrous (∼4 wt.% H2O) basalt in a layered geometry contained in AuPd capsules. All experiments produce melt + fluid + calcite ± clinopyroxene ± plagioclase ± calcic-scapolite ± spinel. With increasing T, plagioclase is progressively replaced by scapolite, clinopyroxene becomes CaTs-rich, and fluid proportion, as inferred from vesicle population, increases. At 1.0 GPa, 1200 °C our hydrous basalt is superliquidus, whereas in the presence of calcite, the experiment produces calcite + clinopyroxene + scapolite + melt. With the consumption of calcite with increasing T and decreasing P, melt, on a volatile-free basis, becomes silica-poor (58.1 wt.% at 1.0 GPa, 1100 °C to 34.9 wt.% at 0.5 GPa, 1200 °C) and CaO-rich (6.7 wt.% at 1.0 GPa, 1100 °C to 43.7 wt.% at 0.5 GPa, 1200 °C), whereas Al2O3 drops (e.g., 19.7 at 1100 °C to 12.8 wt.% at 1200 °C at 1.0 GPa) as clinopyroxene becomes more CaTs-rich. High T or low P melt compositions are ‘ultracalcic,’ potentially presenting a new hypothesis for the origin of ultracalcic melt inclusions in arc lava olivines. Wall-rock calcite consumption is observed to increase with increasing T and decreasing P. At 0.5 GPa, our experiments yield carbonate assimilation from 21.6 to 47.6% between 1100 and 1200 °C. Using measured CO2 outflux rates for Mts. Vesuvius, Merapi, Etna and Popocatepetl over a T variation of 1100 to 1200 °C at 0.5 GPa, we calculate 6–92% of magmatic input estimates undergo this extent of assimilation, suggesting that up to ∼3% of the current global arc CO2 flux may be crustally derived. Application of the assimilation extent bracketed in this study to the estimated elevated number of carbonate-assimilating arc magmatic systems active during the late Cretaceous to early Paleogene suggests that magma-induced upper plate decarbonation alone had the potential to contribute up to 2.7×1014–5.6×1015 g/y CO2, assuming no dilution and complete gaseous release of all assimilated carbon. Using an estimated assimilation extent averaged from current systems gives a slightly lower though still significant value of ≤5.5×1014 g/y of excess CO2 being released into the atmosphere.


SCIENCE: Biological signatures in clumped isotopes of O2

New faculty paper out! See Laurence Yeung’s paper on a new type of biological signature from the “clumping” of rare isotopes in O2, published in Science. [article]


The abundances of molecules containing more than one rare isotope have been applied broadly to determine formation temperatures of natural materials. These applications of “clumped” isotopes rely on the assumption that isotope-exchange equilibrium is reached, or at least approached, during the formation of those materials. In a closed-system terrarium experiment, we demonstrate that biological oxygen (O2) cycling drives the clumped-isotope composition of O2 away from isotopic equilibrium. Our model of the system suggests that unique biological signatures are present in clumped isotopes of O2—and not formation temperatures. Photosynthetic O2 is depleted in 18O18O and 17O18O relative to a stochastic distribution of isotopes, unlike at equilibrium, where heavy-isotope pairs are enriched. Similar signatures may be widespread in nature, offering new tracers of biological and geochemical cycling.

The effects of internal heating and large scale variations on tectonic bi-stability in terrestrial planets

New student paper out! Matt Weller, publishing in Earth and Planetary Science Letters, finds that planets migrate through tectonic states over time as their surface temperatures change. A planet even can have multiple stable tectonic states over time! [article]


We use 3D mantle convection and planetary tectonics models to explore the links between tectonic regimes and the level of internal heating within the mantle of a planet (a proxy for thermal age), planetary surface temperature, and lithosphere strength. At both high and low values of internal heating, for moderate to high lithospheric yield strength, hot and cold stagnant-lid (single plate planet) states prevail. For intermediate values of internal heating, multiple stable tectonic states can exist. In these regions of parameter space, the specific evolutionary path of the system has a dominant role in determining its tectonic state. For low to moderate lithospheric yield strength, mobile-lid behavior (a plate tectonic-like mode of convection) is attainable for high degrees of internal heating (i.e., early in a planet’s thermal evolution). However, this state is sensitive to climate driven changes in surface temperatures. Relatively small increases in surface temperature can be sufficient to usher in a transition from a mobile- to a stagnant-lid regime. Once a stagnant-lid mode is initiated, a return to mobile-lid is not attainable by a reduction of surface temperatures alone. For lower levels of internal heating, the tectonic regime becomes less sensitive to surface temperature changes. Collectively our results indicate that terrestrial planets can alternate between multiple tectonic states over giga-year timescales. Within parameter space regions that allow for bi-stable behavior, any model-based prediction as to the current mode of tectonics is inherently non-unique in the absence of constraints on the geologic and climatic histories of a planet.