Biophysical Systems Research Articles

The Physics of Capitalism

Human economies are complex biophysical systems. By exploring some fundamental concepts in physics, we can develop a better understanding of the ways that the energy-intensive activities of capitalism are changing humanity and the planet.Click here to purchase a PDF version of this article at the Monthly Review website.

Governing Complex Systems: Social Capital for the Anthropocene. Cambridge, MA: The MIT Press. xiii + 279 pages. ISBN 9780262035934, $90.00 hardcover. ISBN 9780262533843, $30.00 paperback. ISBN 9780262338882, $21.00 eBook. Oran R. Young. 2017.

[Extract] Oran Young, a renowned senior scholar in the field of international governance and environmental institutions, has written an ambitious treatise that engages with an important topic of current times––governing complex systems in the era of the Anthropocene. His intention is clear. We are now living in a world of human-dominated ecosystems where the capacity of humans to alter biophysical systems has reached a planetary scale. We must devise innovative governing mechanisms that differ from those already familiar to us and use them as alternatives or supplements to the regulatory approach of dealing with large-scale complex social-ecological phenomena. The need to create governance systems that are nimble or agile, and also adaptable to changing circumstances, is thus palpable. It is in this context that he brings social capital into focus. This stance is encouraging. Yet, the substance with which he promotes his thesis is less dense (and even somewhat disappointing), as he relies on a collection of previously published essays that are refurbished here to connect with the theme of social capital.

HIV as social and ecological experience

The spread and varied impacts of the HIV/AIDS epidemic demonstrate the complex and reciprocal relationships between the socio-political and biophysical dimensions of human health. Yet even with increasing research and policy attention there remain critical gaps in the literature on how HIV-positive households manage health through their engagement with social and ecological systems. This is particularly urgent given improvements in the global response to the epidemic, whereby expanded access to antiretroviral therapy has extended the possibility for survival for years or decades. Because many HIV-positive families and communities in the Global South remain dependent upon a diverse set of resources to generate income and meet subsistence needs, the impacts of disease must be understood within a mix of social processes, including the maintenance of land and collection of natural resources. Similarly, biophysical systems disrupted by HIV/AIDS vary depending upon resource use and locally-specific dynamics that influence opportunities for agrarian production. This paper reports on the findings from a structured survey completed in three communities in northeast South Africa in 2013 that is integrated with focus group discussions and qualitative interviews conducted from 2012–2016. We concentrate upon the diverse ways that individuals and families experience HIV through livelihood systems that are reliant on economic and natural resources. Because the access and use of these resources are mediated by existing social, cultural, and institutional systems, as well as historical spatial economies, we analyze how this produces differential lived experiences for HIV-positive individuals and households in the age of expanded access to antiretroviral therapy.

Open-Boundary Molecular Dynamics of a DNA Molecule in a Hybrid Explicit/Implicit Salt Solution

The composition and electrolyte concentration of the aqueous bathing environment have important consequences for many biological processes and can profoundly affect the behavior of biomolecules. Nevertheless, because of computational limitations, many molecular simulations of biophysical systems can be performed only at specific ionic conditions: either at nominally zero salt concentration, i.e., including only counterions enforcing the system’s electroneutrality, or at excessive salt concentrations. Here, we introduce an efficient molecular dynamics simulation approach for an atomistic DNA molecule at realistic physiological ionic conditions. The simulations are performed by employing the open-boundary molecular dynamics method that allows for simulation of open systems that can exchange mass and linear momentum with the environment. In our open-boundary molecular dynamics approach, the computational burden is drastically alleviated by embedding the DNA molecule in a mixed explicit/implicit salt-bathing solution. In the explicit domain, the water molecules and ions are both overtly present in the system, whereas in the implicit water domain, only the ions are explicitly present and the water is described as a continuous dielectric medium. Water molecules are inserted and deleted into/from the system in the intermediate buffer domain that acts as a water reservoir to the explicit domain, with both water molecules and ions free to enter or leave the explicit domain. Our approach is general and allows for efficient molecular simulations of biomolecules solvated in bathing salt solutions at any ionic strength condition.

A Biophysical Perspective of IPCC Integrated Energy Modelling

The following article conducts an analysis of the Intergovernmental Panel on Climate Change (IPCC) Fifth Assessment Report (AR5), specifically in relation to Integrated Assessment Models (IAMs). We focus on the key drivers of economic growth, how these are derived and whether IAMs properly reflect the underlying biophysical systems. Since baseline IAM scenarios project a three- to eight-fold increase in gross domestic product (GDP)-per-capita by 2100, but with consumption losses of only between 3–11%, strong mitigation seems compatible with economic growth. However, since long-term productivity and economic growth are uncertain, they are included as exogenous parameters in IAM scenarios. The biophysical economics perspective is that GDP and productivity growth are in fact emergent parameters from the economic-biophysical system. If future energy systems were to possess worse biophysical performance characteristics, we would expect lower productivity and economic growth, and therefore, the price of reaching emission targets may be significantly costlier than projected. Here, we show that IAMs insufficiently describe the energy-economy nexus and propose that those key parameters are integrated as feedbacks with the use of environmentally-extended input-output analysis (EEIOA). Further work is required to build a framework that can supplement and support IAM analysis to improve biophysical rigour.

Exploring ship traffic variability off California

Seaborne trade continues to grow and is an important component of the global economy. Threats from shipping to marine ecosystems include oil spills and other water pollution, air pollution, anchor scouring, biological invasions, container loss, chronic noise, and collisions between ships and large whales. Shipping and its associated threats can be influenced by a suite of regulations and economic events. The dynamic nature of ship traffic can be characterized using ship tracking data from automatic identification system (AIS) technology. These data enhance our ability to analyze the ecological threats from commercial shipping as a component of spatially explicit risk assessments. We explore ship traffic variability using a case study in waters off California. AIS data from 2008 to 2015 were used to evaluate the role of vessel emission regulations and economic events on vessel routes and speeds. We document vessels navigating around emission control areas (ECAs) or reducing speed when traveling through them. Large freight vessels decreased speeds from 2008 to 2015 by about 3–6 knots in many areas, with lowered speeds observed in areas of both heavy and sparse vessel use. The timing and location of the speed reductions appear to be most influenced by state and international clean fuel standards, which required the use of more costly fuels. Therefore, the speed reductions may have provided a more cost-effective means of travel. We also found temporary speed increases off southern California when vessels used longer routes to avoid traveling through an ECA. We conclude that the establishment of ECAs had a profound influence on vessel routes and speeds, likely due to the higher costs of clean fuels. Proposals have come before the International Maritime Organization (IMO) to establish clean fuel requirements in various locations around the world to reduce air-borne emissions from vessels. Our research suggests such proposals, or other events that may affect marine fuel prices, can have key impacts on vessel behavior. Consequently, it is important to consider this variability when designing strategies to minimize threats from shipping to vulnerable biophysical systems.

BESS-Rice: A remote sensing derived and biophysical process-based rice productivity simulation model

Conventional process-based crop simulation models and agro-land surface models require numerous forcing variables and input parameters. The regional application of these crop simulation models is complicated by factors concerning input data requirements and parameter uncertainty. In addition, the empirical remotely sensed regional scale crop yield estimation method does not enable growth process modeling. In this study, we developed a process-based rice yield estimation model by integrating an assimilate allocation module into the satellite remote sensing-derived and biophysical process-based Breathing Earth System Simulator (BESS). Normalized accumulated gross primary productivity (GPPnorm-accu) was used as a scaler for growth development, and the relationships between GPPnorm-accu and dry matter partitioning coefficients were determined from the eddy covariance and biometric measurements at the Cheorwon Rice paddy KoFlux site. Over 95% of the variation in the dry matter allocation coefficients of rice grain could be explained by GPPnorm-accu. The dynamics of dry matter distribution among different rice components were simulated, and the annual grain yields were estimated. BESS-Rice simulated GPP and dry matter partitioning dynamics, and rice yields were evaluated against in-situ measurements at three paddy rice sites registered in KoFlux. The results showed that BESS-Rice performed well in terms of rice productivity estimation, with average root mean square error (RMSE) value of 2.2 g C m−2 d−1 (29.5%) and bias of –0.5 g C m−2 d−1 (–7.1%) for daily GPP, and an average RMSE value of 534.8 kg ha−1 (7.7%) and bias of 242.1 kg ha−1 (3.5%) for the annual yield, respectively. BESS-Rice is much simpler than conventional crop models and this helps to reduce the uncertainty related to the forcing variables and input parameters and can result in improved regional yield estimation. The process-based mechanism of BESS-Rice also enables an agronomic diagnosis to be made and the potential impacts of climate change on rice productivity to be investigated.

The Molecular Origin of Enthalpy/Entropy Compensation in Biomolecular Recognition.

Biomolecular recognition can be stubborn; changes in the structures of associating molecules, or the environments in which they associate, often yield compensating changes in enthalpies and entropies of binding and no net change in affinities. This phenomenon-termed enthalpy/entropy (H/S) compensation-hinders efforts in biomolecular design, and its incidence-often a surprise to experimentalists-makes interactions between biomolecules difficult to predict. Although characterizing H/S compensation requires experimental care, it is unquestionably a real phenomenon that has, from an engineering perspective, useful physical origins. Studying H/S compensation can help illuminate the still-murky roles of water and dynamics in biomolecular recognition and self-assembly. This review summarizes known sources of H/ S compensation (real and perceived) and lays out a conceptual framework for understanding and dissecting-and, perhaps, avoiding or exploiting-this phenomenon in biophysical systems.

A Variational Formulation of Nonequilibrium Thermodynamics for Discrete Open Systems with Mass and Heat Transfer.

We propose a variational formulation for the nonequilibrium thermodynamics of discrete open systems, i.e., discrete systems which can exchange mass and heat with the exterior. Our approach is based on a general variational formulation for systems with time-dependent nonlinear nonholonomic constraints and time-dependent Lagrangian. For discrete open systems, the time-dependent nonlinear constraint is associated with the rate of internal entropy production of the system. We show that this constraint on the solution curve systematically yields a constraint on the variations to be used in the action functional. The proposed variational formulation is intrinsic and provides the same structure for a wide class of discrete open systems. We illustrate our theory by presenting examples of open systems experiencing mechanical interactions, as well as internal diffusion, internal heat transfer, and their cross-effects. Our approach yields a systematic way to derive the complete evolution equations for the open systems, including the expression of the internal entropy production of the system, independently on its complexity. It might be especially useful for the study of the nonequilibrium thermodynamics of biophysical systems.

Probabilistic Decision Tools for Determining Impacts of Agricultural Development Policy on Household Nutrition

Governments around the world have agreed to end hunger and food insecurity and to improve global nutrition, largely through changes to agriculture and food systems. However, they are faced with a lot of uncertainty when making policy decisions, since any agricultural changes will influence social and biophysical systems, which could yield either positive or negative nutrition outcomes. We outline a holistic probability modeling approach with Bayesian Network (BN) models for nutritional impacts resulting from agricultural development policy. The approach includes the elicitation of expert knowledge for impact model development, including sensitivity analysis and value of information calculations. It aims at a generalizable methodology that can be applied in a wide range of contexts. To showcase this approach, we develop an impact model of Vision 2040, Uganda's development strategy, which, among other objectives, seeks to transform the country's agricultural landscape from traditional systems to large‐scale commercial agriculture. Model results suggest that Vision 2040 is likely to have negative outcomes for the rural livelihoods it intends to support; it may have no appreciable influence on household hunger but, by influencing preferences for and access to quality nutritional foods, may increase the prevalence of micronutrient deficiency. The results highlight the trade‐offs that must be negotiated when making decisions regarding agriculture for nutrition, and the capacity of BNs to make these trade‐offs explicit. The work illustrates the value of BNs for supporting evidence‐based agricultural development decisions.

Assessing social values of ecosystem services in the Phewa Lake Watershed, Nepal

Community-based forestry (CBF) has developed through co-evolution of human societies, social values and biophysical systems shaped by long-term community activities. CBF has been practised for nearly 40 years in Nepal and has resulted in the restoration of forest cover to a considerable proportion of the mountain regions. In the Phewa watershed, restored forests are important for the subsistence of local communities and the provision of economically valuable recreation, aesthetic and cultural services for a wider group of stakeholders. In that context, this study aims to assess the social values of ecosystem services (ES) and their relative importance to different stakeholders. Community perceptions and expert opinions to assess and prioritise ES in the watershed were sought through focus group discussions and key informant surveys. There were 23 ecosystem services relevant to the local communities and other stakeholders in the watershed. Sediment retention, recreation and ecotourism, freshwater, firewood and timber were priority ES for local benefits, while recreation and ecotourism, biodiversity maintenance, sediment retention and carbon stock were priority ES for wider (regional – global) benefits. Priority ES revealed key areas of correlation and conflict between different services and between stakeholder groups. For local benefits, trade-offs were identified between provisioning services and regulating, habitat and cultural services. Synergies were predominant between regulating, cultural and habitat services. The study indicated that the social values concept is a promising tool for eliciting people's preferences in the ES assessment and analysis of trade-offs and synergies in developing countries where community involvement is the dominant approach of forest management.

Shrinking greenery: Land use and land cover changes in Kurram Agency, Kohi Safid Mountains of north-western Pakistan

Deforestation and other Land Use and Land Cover (LULC) changes, driven by variety of physical and anthropogenic factors, have altered the mountainous environment. Mountains around the world including northern and north western belts of Pakistan are highly sensitive to deforestation and other LULC changes, which have profound impacts on various sectors of bio-physical and socio-economic systems. Assessment of LULC changes has high significance for protection, conservation and monitoring mountainous environment. The present study is an attempt to assess the landscape changes with particular reference to forest cover depletion in Kurram Agency located in the north western mountain belt of Pakistan. For detailed comparative analysis the study area has been divided into three sections, which coincide with the present administrative divisions of the Agency, i.e., Upper, Lower and Central Kurram. Temporal span of this study covers four decades. In this study, land use map of 1970 and land sat satellite imageries of 1987, 2000 and 2014 were used as spatial data sets. The images were processed and classified into six LULC classes through geospatial packages and change detection maps were prepared for each division and time period. Findings of the study reveal two trends in the four major LULC categories. Forest and rangeland have shrunk, on average, by 15% and 7.5% respectively while, bare soil and rocks outcrops have expanded by 89% and agriculture land by 7.2% in Kurram agency. The water bodies and snow cover have minor fluctuation in its land area. Major causes of shrinking greenery is attributed to high influx of Afghan refugees and high energy demand of growing population. However, with outflow of the refugees from Kurram agency the general trend in forest cover has reverted and deforestation rate has slowed down.

Asymptotic Analysis on Dielectric Boundary Effects of Modified Poisson--Nernst--Planck Equations

The charge transport in an environment with inhomogeneous dielectric permittivity is ubiquitous in many areas such as electrochemical energy devices and biophysical systems. We theoretically study ...

Ecological Crisis and the Problem of How to Inhabit a Norm

The Anthropocene is distinguished by the knowledge that collective human action is damaging the earth's biophysical systems in a manner that has serious implications for human life and nature. In a recent work, Dale Jamieson has argued that despite this knowledge moral philosophy is limited in its capacity to provide the wholesale re-orientation of human practices that are required if humanity is to respond successfully to the array of ecological crises that have emerged in the Anthropocene. This paper will argue that the role second nature plays in ethical formation provides a better prospect for understanding normative change than moral philosophy, because it allows for an appreciation of the ways in which norms are embodied and for the objective conditions that make such change possible.

Soil Carbon Sequestration Differentials among Key Forest Plantation Species in Kenya: Promising Opportunities for Sustainable Development Mechanism

Soil organic carbon (SOC) contributes to the productivity of forests and enhances carbon sink in forest ecosystem. However, the available data on forest based carbon projects among African countries that have ratified Kyoto Protocol and are party to United Nations Framework Convention on Climate Change (UNFCCC) shows little emphasis on SOC, deadwood and litter. Kenya, for example, has piloted five afforestation and reforestation Clean Development Mechanism (AR-CDM) activities in government forests of which none addresses SOC, and yet studies elsewhere have shown that forest soils consist about 73 % of global carbon storage. This study therefore, sought to determine soil carbon sequestration differentials among selected key forest plantations in Kenya and their future implications on sustainable development mechanism. Soils were sampled at 0-20, 20-50 and 50-80 cm depth from Pinus patula, Cupressus lusitanica, Juniperus procera and Eucalyptus saligna/grandis plantations in Central Kenya for analysis of carbon, soil pH, nitrogen, phosphorous and potassium. The litter-fall collected from each of these forest plantations were analysed for nitrogen and carbon. The Pinus patula plantations had significantly (p<0.01) higher amount of soil carbon (132.2 ± 12.55 MgC ha-1) as compared with Cupressus lusitanica (114.4 ± 12.55 MgC ha-1) and Eucalyptus saligna (85.0 ± 12.55 MgC ha-1) plantations. Specifically, Pinus patula plantation had sequestered almost twice of soil carbon as compared to above and below-ground carbon pools whereas that of Cupressus lusitanica and Eucalyptus saligna /grandis were about 1.2 and 1.3 times higher, respectively. The levels of acidity varied among species, between and within sites from very strongly acidic to very slightly acidic. The amount of soil nitrogen, phosphorous and potassium between sites, tree species and soil depths differed significantly. This study therefore reveals soil carbon potentials in forest plantations that need to be considered in the development and implementation of afforestation and reforestation activities under Clean/Sustainable Development Mechanism (SDM). Equally, differences on soil carbon sequestered among species need to be taken into account when evaluating carbon stocks under certified and voluntary carbon offset markets in order to promote trees with high potential of carbon sequestration for sustainable development. This is important because, introduction of Reducing Emissions from Deforestation and forest Degradation (REDD+) and forest based Clean Development Mechanisms (CDM) have provided impetus to African governments in implementing afforestation and reforestation (AR) programmes to enhance carbon stock and improve resilience of biophysical and social systems against impacts of climate of change.

Equilibrium structure and diffusion in concentrated hydrodynamically interacting suspensions confined by a spherical cavity

The short- and long-time equilibrium transport properties of a hydrodynamically interacting suspension confined by a spherical cavity are studied via Stokesian dynamics simulations for a wide range of particle-to-cavity size ratios and particle concentrations. Many-body hydrodynamic and lubrication interactions between particles and with the cavity are accounted for utilizing recently developed mobility and resistance tensors for spherically confined suspensions (Aponte-Rivera &amp; Zia, Phys. Rev. Fluids, vol. 1(2), 2016, 023301). Study of particle volume fractions in the range $0.05\leqslant \unicode[STIX]{x1D719}\leqslant 0.40$ reveals that confinement exerts a qualitative influence on particle diffusion. First, the mean-square displacement over all time scales depends on the position in the cavity. Additionally, at short times, the diffusivity is anisotropic, with diffusion along the cavity radius slower than diffusion tangential to the cavity wall, due to the anisotropy of hydrodynamic coupling and to confinement-induced spatial heterogeneity in particle concentration. The mean-square displacement is anisotropic at intermediate times as well and, surprisingly, exhibits superdiffusive and subdiffusive behaviours for motion along and perpendicular to the cavity radius respectively, depending on the suspension volume fraction and the particle-to-cavity size ratio. No long-time self-diffusive regime exists; instead, the mean-square displacement reaches a long-time plateau, a result of entropic restriction to a finite volume. In this long-time limit, the higher the volume fraction is, the longer the particles take to reach the long-time plateau, as cooperative rearrangements are required as the cavity becomes crowded. The ordered dynamical heterogeneity seen here promotes self-organization of particles based on their size and self-mobility, which may be of particular relevance in biophysical systems.

A Conceptual Model for Land System Dynamics as a Coupled Human–Environment System

This paper presents a conceptual model of land as a coupled human–environment system. Land use and land cover are incorporated as elements of the human and environment system respectively. Drivers and associated processes that influence land use, land cover, and land system dynamics are incorporated within a set of sub-systems. The model includes consideration of driving sub-systems as a set of capital funds and flows, and how these are influenced by linkages between processes in the human (socio-economic) and environment systems and sub-systems. The model is consistent with existing models of the biophysical earth system used by the land change, earth system sciences, and socio-ecological systems communities. The purposes of the model are to provide (i) a holistic framework within which descriptions, models and analyses that focus on various components of land can be placed to describe and explain land systems and land system changes; and (ii) a guide for the development of more fully integrated and interdisciplinary understanding, analysis and study of land use and land cover dynamics, with explicit focus on relationships between human and natural systems.

Single Molecule Force Spectroscopy and Molecular Dynamics Simulations as a Combined Platform for Probing Protein Face-Specific Binding

Biomolecular interactions frequently occur in orientation-specific manner. For example, prior nuclear magnetic resonance spectroscopy experiments in our lab have suggested the presence of a group of strongly binding residues on a particular face of the protein ubiquitin for interactions with Capto MMC multimodal ligands ("Capto" ligands) (Srinivasan, K.; et al. Langmuir 2014, 30 (44), 13205-13216). We present a clear confirmation of those studies by performing single-molecule force spectroscopy (SMFS) measurements of unbinding complemented with molecular dynamics (MD) calculations of the adsorption free energy of ubiquitin in two distinct orientations with self-assembled monolayers (SAMs) functionalized with "Capto" ligands. These orientations were maintained in the SMFS experiments by tethering ubiquitin mutants to SAM surfaces through strategically located cysteines, thus exposing the desired faces of the protein. Analogous orientations were maintained in MD simulations using suitable constraining methods. Remarkably, despite differences between the finer details of experimental and simulation methodologies, they confirm a clear preference for the previously hypothesized binding face of ubiquitin. Furthermore, MD simulations provided significant insights into the mechanism of protein binding onto this multimodal surface. Because SMFS and MD simulations both directly probe protein-surface interactions, this work establishes a key link between experiments and simulations at molecular scale through the determination of protein face-specific binding energetics. Our approach may have direct applications in biophysical systems where face- or orientation-specific interactions are important, such as biomaterials, sensors, and biomanufacturing.

The Biophysical Effects of Neolithic Island Colonization: General Dynamics and Sociocultural Implications

Does anthropogenic environmental change constrain long-term sociopolitical outcomes? It is clear that human colonization of islands radically alters their biological and physical systems. Despite considerable contextual variability in local specificities of this alteration, I argue that these processes are to some extent regular, predictable, and have socio-political implications. Reviewing the data for post-colonization ecodynamics, I show that Neolithic colonization of previously insulated habitats drives biotic homogenization. I argue that we should expect such homogenization to promote regular types of change in biophysical systems, types of change that can be described in sum as environmentally convergent. Such convergence should have significant implications for human social organization over the long term, and general dynamics of this sort are relevant in the context of understanding remarkably similar social evolutionary trajectories towards wealth-inequality not only islands, but also more generally.

The sociological imagination in a time of climate change

Abstract Despite rising calls for social science knowledge in the face of climate change, too few sociologists have been engaged in the conversations about how we have arrived at such perilous climatic circumstances, or how society can change course. With its attention to the interactive dimensions of social order between individuals, social norms, cultural systems and political economy, the discipline of sociology is uniquely positioned to be an important leader in this conversation. In this paper I suggest that in order to understand and respond to climate change we need two kinds of imagination: 1) to see the relationships between human actions and their impacts on earth's biophysical system (ecological imagination) and 2) to see the relationships within society that make up this environmentally damaging social structure (sociological imagination). The scientific community has made good progress in developing our ecological imagination but still need to develop a sociological imagination. The application of a sociological imagination allows for a powerfully reframing of four key problems in the current interdisciplinary conversation on climate change: why climate change is happening, how we are being impacted, why we have failed to successfully respond so far, and how we might be able to effectively do so . I visit each of these four questions describing the current understanding and show the importance of the sociological imagination and other insights from the field of sociology. I close with reflections on current limitations in sociology's potential to engage climate change and the Anthropocene.