Scripps Institution of Oceanography

The planetary boundaries framework defines a safe operating space for humanity based on the intrinsic biophysical processes that regulate the stability of the Earth system. Here, we revise and update the planetary boundary framework, with a focus on the underpinning biophysical science, based on targeted input from expert research communities and on more general scientific advances over the past 5 years. Several of the boundaries now have a two-tier approach, reflecting the importance of cross-scale interactions and the regional-level heterogeneity of the processes that underpin the boundaries. Two core boundaries—climate change and biosphere integrity—have been identified, each of which has the potential on its own to drive the Earth system into a new state should they be substantially and persistently transgressed.

Ecological extinction caused by overfishing precedes all other pervasive human disturbance to coastal ecosystems, including pollution, degradation of water quality, and anthropogenic climate change. Historical abundances of large consumer species were fantastically large in comparison with recent observations. Paleoecological, archaeological, and historical data show that time lags of decades to centuries occurred between the onset of overfishing and consequent changes in ecological communities, because unfished species of similar trophic level assumed the ecological roles of overfished species until they too were overfished or died of epidemic diseases related to overcrowding. Retrospective data not only help to clarify underlying causes and rates of ecological change, but they also demonstrate achievable goals for restoration and management of coastal ecosystems that could not even be contemplated based on the limited perspective of recent observations alone.

AutoDock Vina is arguably one of the fastest and most widely used open-source programs for molecular docking. However, compared to other programs in the AutoDock Suite, it lacks support for modeling specific features such as macrocycles or explicit water molecules. Here, we describe the implementation of these functionality in AutoDock Vina 1.2.0. Additionally, AutoDock Vina 1.2.0 supports the AutoDock4.2 scoring function, simultaneous docking of multiple ligands, and a batch mode for docking a large number of ligands. Furthermore, we implemented Python bindings to facilitate scripting and the development of docking workflows. This work is an effort toward the unification of the features of the AutoDock4 and AutoDock Vina programs. The source code is available at https://github.com/ccsb-scripps/AutoDock-Vina

The NCEP–DOE Atmospheric Model Intercomparison Project (AMIP-II) reanalysis is a follow-on project to the “50-year” (1948–present) NCEP–NCAR Reanalysis Project. NCEP–DOE AMIP-II re-analysis covers the “20-year” satellite period of 1979 to the present and uses an updated forecast model, updated data assimilation system, improved diagnostic outputs, and fixes for the known processing problems of the NCEP–NCAR reanalysis. Only minor differences are found in the primary analysis variables such as free atmospheric geopotential height and winds in the Northern Hemisphere extratropics, while significant improvements upon NCEP–NCAR reanalysis are made in land surface parameters and land–ocean fluxes. This analysis can be used as a supplement to the NCEP–NCAR reanalysis especially where the original analysis has problems. The differences between the two analyses also provide a measure of uncertainty in current analyses.

Recently developed techniques for estimating bacterial biomass and productivity indicate that bacterial biomass in the sea is related to phytoplankton concentration and that bacteria utilise 10 to 50 % of carbon fixed by photosynthesis. Evidence is presented to suggest that numbers of free bacteria are controlled by nanoplankton~c heterotrophic flagellates which are ubiquitous in the marine water column. The flagellates in turn are preyed upon by microzooplankton. Heterotrophic flagellates and microzooplankton cover the same size range as the phytoplankton, thus providing the means for returning some energy from the 'microbial loop' to the conventional planktonic food chain.

Western United States forest wildfire activity is widely thought to have increased in recent decades, yet neither the extent of recent changes nor the degree to which climate may be driving regional changes in wildfire has been systematically documented. Much of the public and scientific discussion of changes in western United States wildfire has focused instead on the effects of 19th- and 20th-century land-use history. We compiled a comprehensive database of large wildfires in western United States forests since 1970 and compared it with hydroclimatic and land-surface data. Here, we show that large wildfire activity increased suddenly and markedly in the mid-1980s, with higher large-wildfire frequency, longer wildfire durations, and longer wildfire seasons. The greatest increases occurred in mid-elevation, Northern Rockies forests, where land-use histories have relatively little effect on fire risks and are strongly associated with increased spring and summer temperatures and an earlier spring snowmelt.

This review covers the literature published in 2008 for marine natural products, with 829 citations (613 for the period January to December 2008) referring to compounds isolated from marine microorganisms and phytoplankton, green algae, brown algae, red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1065 for 2008), together with the relevant biological activities, source organisms and country of origin. Biosynthetic studies, first syntheses, and syntheses that lead to the revision of structures or stereochemistries, have been included.

A digital bathymetric map of the oceans with a horizontal resolution of 1 to 12 kilometers was derived by combining available depth soundings with high-resolution marine gravity information from the Geosat and ERS-1 spacecraft. Previous global bathymetric maps lacked features such as the 1600-kilometer-long Foundation Seamounts chain in the South Pacific. This map shows relations among the distributions of depth, sea floor area, and sea floor age that do not fit the predictions of deterministic models of subsidence due to lithosphere cooling but may be explained by a stochastic model in which randomly distributed reheating events warm the lithosphere and raise the ocean floor.

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

A method is described which permits measurement of sap pressure in the xylem of vascular plants. As long predicted, sap pressures during transpiration are normally negative, ranging from -4 or -5 atmospheres in a damp forest to -80 atmospheres in the desert. Mangroves and other halophytes maintain at all times a sap pressure of -35 to -60 atmospheres. Mistletoes have greater suction than their hosts, usually by 10 to 20 atmospheres. Diurnal cycles of 10 to 20 atmospheres are common. In tall conifers there is a hydrostatic pressure gradient that closely corresponds to the height and seems surprisingly little influenced by the intensity of transpiration. Sap extruded from the xylem by gas pressure on the leaves is practically pure water. At zero turgor this procedure gives a linear relation between the intracellular concentration and the tension of the xylem.

When creating camera‐ready figures, most scientists are familiar with the sequence of raw data → processing → final illustration and with the spending of large sums of money to finalize papers for submission to scientific journals, prepare proposals, and create overheads and slides for various presentations. This process can be tedious and is often done manually, since available commercial or in‐house software usually can do only part of the job. To expedite this process, we introduce the Generic Mapping Tools (GMT), which is a free, public domain software package that can be used to manipulate columns of tabular data, time series, and gridded data sets and to display these data in a variety of forms ranging from simple x‐y plots to maps and color, perspective, and shaded‐relief illustrations. GMT uses the PostScript page description language, which can create arbitrarily complex images in gray tones or 24‐bit true color by superimposing multiple plot files. Line drawings, bitmapped images, and text can be easily combined in one illustration. PostScript plot files are device‐independent, meaning the same file can be printed at 300 dots per inch (dpi) on an ordinary laserwriter or at 2470 dpi on a phototypesetter when ultimate quality is needed. GMT software is written as a set of UNIX tools and is totally self contained and fully documented. The system is offered free of charge to federal agencies and nonprofit educational organizations worldwide and is distributed over the computer network Internet.

Human activities are releasing tiny particles (aerosols) into the atmosphere. These human-made aerosols enhance scattering and absorption of solar radiation. They also produce brighter clouds that are less efficient at releasing precipitation. These in turn lead to large reductions in the amount of solar irradiance reaching Earth's surface, a corresponding increase in solar heating of the atmosphere, changes in the atmospheric temperature structure, suppression of rainfall, and less efficient removal of pollutants. These aerosol effects can lead to a weaker hydrological cycle, which connects directly to availability and quality of fresh water, a major environmental issue of the 21st century.

Until recently, large apex consumers were ubiquitous across the globe and had been for millions of years. The loss of these animals may be humankind's most pervasive influence on nature. Although such losses are widely viewed as an ethical and aesthetic problem, recent research reveals extensive cascading effects of their disappearance in marine, terrestrial, and freshwater ecosystems worldwide. This empirical work supports long-standing theory about the role of top-down forcing in ecosystems but also highlights the unanticipated impacts of trophic cascades on processes as diverse as the dynamics of disease, wildfire, carbon sequestration, invasive species, and biogeochemical cycles. These findings emphasize the urgent need for interdisciplinary research to forecast the effects of trophic downgrading on process, function, and resilience in global ecosystems.

The diversity, frequency, and scale of human impacts on coral reefs are increasing to the extent that reefs are threatened globally. Projected increases in carbon dioxide and temperature over the next 50 years exceed the conditions under which coral reefs have flourished over the past half-million years. However, reefs will change rather than disappear entirely, with some species already showing far greater tolerance to climate change and coral bleaching than others. International integration of management strategies that support reef resilience need to be vigorously implemented, and complemented by strong policy decisions to reduce the rate of global warming.

Recent climatic changes have enhanced plant growth in northern mid-latitudes and high latitudes. However, a comprehensive analysis of the impact of global climatic changes on vegetation productivity has not before been expressed in the context of variable limiting factors to plant growth. We present a global investigation of vegetation responses to climatic changes by analyzing 18 years (1982 to 1999) of both climatic data and satellite observations of vegetation activity. Our results indicate that global changes in climate have eased several critical climatic constraints to plant growth, such that net primary production increased 6% (3.4 petagrams of carbon over 18 years) globally. The largest increase was in tropical ecosystems. Amazon rain forests accounted for 42% of the global increase in net primary production, owing mainly to decreased cloud cover and the resulting increase in solar radiation.

The discrete-dipole approximation (DDA) for scattering calculations, including the relationship between the DDA and other methods, is reviewed. Computational considerations, i.e., the use of complex-conjugate gradient algorithms and fast-Fourier-transform methods, are discussed. We test the accuracy of the DDA by using the DDA to compute scattering and absorption by isolated, homogeneous spheres as well as by targets consisting of two contiguous spheres. It is shown that, for dielectric materials (|m| ≲ 2), the DDA permits calculations of scattering and absorption that are accurate to within a few percent.

Oxygen is fundamental to life. Not only is it essential for the survival of individual animals, but it regulates global cycles of major nutrients and carbon. The oxygen content of the open ocean and coastal waters has been declining for at least the past half-century, largely because of human activities that have increased global temperatures and nutrients discharged to coastal waters. These changes have accelerated consumption of oxygen by microbial respiration, reduced solubility of oxygen in water, and reduced the rate of oxygen resupply from the atmosphere to the ocean interior, with a wide range of biological and ecological consequences. Further research is needed to understand and predict long-term, global- and regional-scale oxygen changes and their effects on marine and estuarine fisheries and ecosystems.

Abstract The inversion of electromagnetic sounding data does not yield a unique solution, but inevitably a single model to interpret the observations is sought. We recommend that this model be as simple, or smooth, as possible, in order to reduce the temptation to overinterpret the data and to eliminate arbitrary discontinuities in simple layered models.To obtain smooth models, the nonlinear forward problem is linearized about a starting model in the usual way, but it is then solved explicitly for the desired model rather than for a model correction. By parameterizing the model in terms of its first or second derivative with depth, the minimum norm solution yields the smoothest possible model.Rather than fitting the experimental data as well as possible (which maximizes the roughness of the model), the smoothest model which fits the data to within an expected tolerance is sought. A practical scheme is developed which optimizes the step size at each iteration and retains the computational efficiency of layered models, resulting in a stable and rapidly convergent algorithm. The inversion of both magnetotelluric and Schlumberger sounding field data, and a joint magnetotelluric-resistivity inversion, demonstrate the method and show it to have practical application.

Understanding and quantifying the global methane (CH4) budget is important for assessing realistic pathways to mitigate climate change. Atmospheric emissions and concentrations of CH4 continue to increase, making CH4 the second most important human-influenced greenhouse gas in terms of climate forcing, after carbon dioxide (CO2). The relative importance of CH4 compared to CO2 depends on its shorter atmospheric\nlifetime, stronger warming potential, and variations in atmospheric growth rate over the past decade, the causes of which are still debated. Two major challenges in reducing uncertainties in the atmospheric growth rate arise from the variety of geographically overlapping CH4 sources and from the destruction of CH4 by short-lived hydroxyl radicals (OH). To address these challenges, we have established a consortium of multidisciplinary scientists under the umbrella of the Global Carbon Project to synthesize and stimulate new research aimed at improving and regularly updating the global methane budget. Following Saunois et al. (2016), we present here the second version of the living review paper dedicated to the decadal methane budget, integrating results of top-down studies (atmospheric observations within an atmospheric inverse-modelling framework) and bottom-up estimates (including process-based models for estimating land surface emissions and atmospheric chemistry, inventories of anthropogenic emissions, and data-driven extrapolations).\nFor the 2008–2017 decade, global methane emissions are estimated by atmospheric inversions (a top-down approach) to be 576 TgCH4 yr-1 (range 550–594, corresponding to the minimum and maximum estimates of the model ensemble). Of this total, 359 TgCH4 yr-1 or 60% is attributed to anthropogenic sources, that is emissions caused by direct human activity (i.e. anthropogenic emissions; range 336–376 TgCH4 yr-1 or 50 %–65 %). The mean annual total emission for the new decade (2008–2017) is 29 TgCH4 yr-1 larger than our estimate for the previous decade (2000–2009), and 24 TgCH4 yr-1 larger than the one reported in the previous budget for 2003–2012 (Saunois et al., 2016). Since 2012, global CH4 emissions have been tracking the warmest scenarios assessed by the Intergovernmental Panel on Climate Change. Bottom-up methods suggest almost 30% larger global emissions (737 TgCH4 yr-1, range 594–881) than top-down inversion methods. Indeed, bottom-up estimates for natural sources such as natural wetlands, other inland water systems, and geological sources are higher than top-down estimates. The atmospheric constraints on the top-down budget suggest that at least some of these bottom-up emissions are overestimated. The latitudinal distribution of atmospheric observation-based emissions indicates a predominance of tropical emissions (∼65% of the global budget, <30◦N) compared to mid-latitudes (∼30 %, 30–60◦ N) and high northern latitudes (∼4 %, 60–90◦N). The most important source of uncertainty in the methane budget is attributable to natural emissions, especially those from wetlands and other inland waters.\nSome of our global source estimates are smaller than those in previously published budgets (Saunois et al., 2016; Kirschke et al., 2013). In particular wetland emissions are about 35 TgCH4 yr-1 lower due to improved partition wetlands and other inland waters. Emissions from geological sources and wild animals are also found to be smaller by 7 TgCH4 yr-1 by 8 TgCH4 yr-1, respectively. However, the overall discrepancy between bottom-up and top-down estimates has been reduced by only 5% compared to Saunois et al. (2016), due to a higher estimate of emissions from inland waters, highlighting the need for more detailed research on emissions factors. Priorities for improving the methane budget include (i) a global, high-resolution map of water-saturated soils and inundated areas emitting methane based on a robust classification of different types of emitting habitats; (ii) further development of process-based models for inland-water emissions; (iii) intensification of methane observations at local scales (e.g., FLUXNET-CH4 measurements) and urban-scale monitoring to constrain bottom-up land surface models, and at regional scales (surface networks and satellites) to constrain atmospheric inversions; (iv) improvements of transport models and the representation of photochemical sinks in top-down inversions; and (v) development of a 3D variational inversion system using isotopic and/or co-emitted species such as ethane to improve source partitioning.\nThe data presented here can be downloaded from https://doi.org/10.18160/GCP-CH4-2019 (Saunois et al.,\n2020) and from the Global Carbon Project

A method is developed for interpreting the statistics of the sun’s glitter on the sea surface in terms of the statistics of the slope distribution. The method consists of two principal phases: (1) of identifying, from geometric considerations, any point on the surface with the particular slope required for the reflection of the” sun’s rays toward the observer; and (2) of interpreting the average brightness of the sea surface in the vicinity of this point in terms of the frequency with which this particular slope occurs. The computation of the probability of large (and infrequent) slopes is limited by the disappearance of the glitter into a background consisting of (1) the sunlight scattered from particles beneath the sea surface, and (2) the skylight reflected by the sea surface.The method has been applied to aerial photographs taken under carefully chosen conditions in the Hawaiian area. Winds were measured from a vessel at the time and place of the aerial photographs, and cover a range from 1 to 14 m sec−1. The effect of surface slicks, laid by the vessel, are included in the study. A two-dimensional Gram-Charlier series is fitted to the data. As a first approximation the distribution is Gaussian and isotropic with respect to direction. The mean square slope (regardless of direction) increases linearly with the wind speed, reaching a value of (tan16°)2 for a wind speed of 14 m sec−1. The ratio of the up/ downwind to the crosswind component of mean square slope varies from 1.0 to 1.9. There is some up/downwind skewness which increases with increasing wind speed. As a result the most probable slope at high winds is not zero but a few degrees, with the azimuth of ascent pointing downwind. The measured peakedness which is barely above the limit of observational error, is such as to make the probability of very large and very small slopes greater than Gaussian. The effect of oil slicks covering an area of one-quarter square mile is to reduce the mean square slopes by a factor of two or three, to eliminate skewness, but to leave peakedness unchanged.