The genomic program for development operates primarily by the regulated expression of genes encoding transcription factors and components of cell signaling pathways. This program is executed by cis-regulatory DNAs (e.g., enhancers and silencers) that control gene expression. The regulatory inputs and functional outputs of developmental control genes constitute network-like architectures. In this PNAS Special Feature are assembled papers on developmental gene regulatory networks governing the formation of various tissues and organs in nematodes, flies, sea urchins, frogs, and mammals. Here, we survey salient points of these networks, by using as reference those governing specification of the endomesoderm in sea urchin embryos and dorsal–ventral patterning in the Drosophila embryo.
In the past half century, radioastronomy has changed our perception and understanding of the universe. In this issue of PNAS, the molecular chemistry directly observed within the galaxy is discussed. For the most part, the description of the molecular transformations requires specific kinetic schemes rather than chemical thermodynamics. Ionization of the very abundant molecular hydrogen and atomic helium followed by their secondary reactions is discussed. The rich variety of organic species observed is a challenge for complete understanding. The role and nature of reactions involving grain surfaces as well as new spectroscopic observations of interstellar and circumstellar regions are topics presented in this special feature.
During the process of biological nitrogen fixation, the enzyme nitrogenase catalyzes the ATP-dependent reduction of dinitrogen to ammonia. Nitrogenase consists of two component metalloproteins, the iron (Fe) protein and the molybdenum-iron (MoFe) protein; the Fe protein mediates the coupling of ATP hydrolysis to interprotein electron transfer, whereas the active site of the MoFe protein contains the polynuclear FeMo cofactor, a species composed of seven iron atoms, one molybdenum atom, nine sulfur atoms, an interstitial light atom, and one homocitrate molecule. This Perspective provides an overview of biological nitrogen fixation and introduces three contributions to this special feature that address central aspects of the mechanism and assembly of nitrogenase.
This Perspective on multidimensional spectroscopy in the optical and infrared spectral regions focuses on the principles and the scientific and technical challenges facing these new fields. The methods hold great promise for advances in the visualization of time-dependent structural changes in complex systems ranging from liquids to biological assemblies, new materials, and fundamental physical processes. The papers in this special feature on multidimensional spectroscopy in chemistry, physics, and biology are typical of many recent advances.
In the context of governance of human–environment interactions, a panacea refers to a blueprint for a single type of governance system (e.g., government ownership, privatization, community property) that is applied to all environmental problems. The aim of this special feature is to provide theoretical analysis and empirical evidence to caution against the tendency, when confronted with pervasive uncertainty, to believe that scholars can generate simple models of linked social–ecological systems and deduce general solutions to the overuse of resources. Practitioners and scholars who fall into panacea traps falsely assume that all problems of resource governance can be represented by a small set of simple models, because they falsely perceive that the preferences and perceptions of most resource users are the same. Readers of this special feature will become acquainted with many cases in which panaceas fail. The articles provide an excellent overview of why they fail. Furthermore, the articles in this special feature address how scholars and public officials can increase the prospects for future sustainable resource use by facilitating a diagnostic approach in selecting appropriate starting points for governance and monitoring, as well as by learning from the outcomes of new policies and adapting in light of effective feedback.
The articles in this special feature challenge the presumption that scholars can make simple, predictive models of social–ecological systems (SESs) and deduce universal solutions, panaceas, to problems of overuse or destruction of resources. Moving beyond panaceas to develop cumulative capacities to diagnose the problems and potentialities of linked SESs requires serious study of complex, multivariable, nonlinear, cross-scale, and changing systems. Many variables have been identified by researchers as affecting the patterns of interactions and outcomes observed in empirical studies of SESs. A step toward developing a diagnostic method is taken by organizing these variables in a nested, multitier framework. The framework enables scholars to organize analyses of how attributes of (i) a resource system (e.g., fishery, lake, grazing area), (ii) the resource units generated by that system (e.g., fish, water, fodder), (iii) the users of that system, and (iv) the governance system jointly affect and are indirectly affected by interactions and resulting outcomes achieved at a particular time and place. The framework also enables us to organize how these attributes may affect and be affected by larger socioeconomic, political, and ecological settings in which they are embedded...
Land change science has emerged as a fundamental component of global environmental change and sustainability research. This interdisciplinary field seeks to understand the dynamics of land cover and land use as a coupled human–environment system to address theory, concepts, models, and applications relevant to environmental and societal problems, including the intersection of the two. The major components and advances in land change are addressed: observation and monitoring; understanding the coupled system—causes, impacts, and consequences; modeling; and synthesis issues. The six articles of the special feature are introduced and situated within these components of study.
Understanding the motions of the constituent atoms in reacting molecules lies at the heart of chemistry and is the central focus of chemical reaction dynamics. The most detailed questions one can ask are about the evolution of molecules prepared in a single quantum state to products in individual states, and both calculations and experiments are providing such detailed understanding of increasingly complex systems. A central goal of these studies is uncovering the essential details of chemical change by removing the averaging over the initial conditions that occurs in many cases. Such information provides an exquisite test of theory and helps paint pictures of complicated chemical transformations. The goal of this Special Feature is to provide a snapshot of a portion of the field of chemical reaction dynamics. Much of the work presented here emphasizes a close interplay of experiment and theory in ways that sharpen the conclusions of both and animate future studies. The articles do not completely cover the rich field of chemical reaction dynamics but rather provide a glimpse of some of the emerging insights.
Movement of individual organisms is fundamental to life, quilting our planet in a rich tapestry of phenomena with diverse implications for ecosystems and humans. Movement research is both plentiful and insightful, and recent methodological advances facilitate obtaining a detailed view of individual movement. Yet, we lack a general unifying paradigm, derived from first principles, which can place movement studies within a common context and advance the development of a mature scientific discipline. This introductory article to the Movement Ecology Special Feature proposes a paradigm that integrates conceptual, theoretical, methodological, and empirical frameworks for studying movement of all organisms, from microbes to trees to elephants. We introduce a conceptual framework depicting the interplay among four basic mechanistic components of organismal movement: the internal state (why move?), motion (how to move?), and navigation (when and where to move?) capacities of the individual and the external factors affecting movement. We demonstrate how the proposed framework aids the study of various taxa and movement types; promotes the formulation of hypotheses about movement; and complements existing biomechanical, cognitive, random, and optimality paradigms of movement. The proposed framework integrates eclectic research on movement into a structured paradigm and aims at providing a basis for hypothesis generation and a vehicle facilitating the understanding of the causes...
The field of marine reserve science has matured greatly over the last decade, moving beyond studies of single reserves and beyond perspectives from single disciplines. This Special Feature exemplifies recent advances in marine reserve research, showing insights gained from synthetic studies of reserve networks, long-term changes within reserves, integration of social and ecological science research, and balance between reserve design for conservation as well as fishery and other commercial objectives. This rich body of research helps to inform conservation planning for marine ecosystems but also poses new challenges for further study, including how to best design integrated fisheries management and conservation systems, how to effectively evaluate the performance of entire reserve networks, and how to examine the complex coupling between ecological and socioeconomic responses to reserve networks.
Increasing food production and mitigating climate change are two primary but seemingly contradictory objectives for tropical landscapes. This special feature examines synergies and trade-offs among these objectives. Four themes emerge from the papers: the important roles of both forest and agriculture sectors for climate mitigation in tropical countries; the minor contribution from deforestation-related agricultural expansion to overall food production at global and continental scales; the opportunities for synergies between improved food production and reductions in greenhouse gas emissions through diversion of agricultural expansion to already-cleared lands, improved soil, crop, and livestock management, and agroforestry; and the need for targeted policy and management interventions to make these synergistic opportunities a reality. We conclude that agricultural intensification is a key factor to meet dual objectives of food production and climate mitigation, but there is no single panacea for balancing these objectives in all tropical landscapes. Place-specific strategies for sustainable land use emerge from assessments of current land use, demographics, and other biophysical and socioeconomic characteristics, using a whole-landscape...
The use of small-molecule organic catalysts in organic synthesis has flourished over the past decade. Examples of defining concepts and cutting-edge results are provided in the papers in this Special Feature.
Since a comprehensive understanding of brain function and evolution in vertebrates is often hobbled by the sheer size of the nervous system, as well as ethical concerns, major research efforts have been made to understand the neural circuitry underpinning behaviour and cognition in invertebrates, and its costs and benefits under natural conditions. This special feature of Proceedings of the Royal Society B contains an idiosyncratic range of current research perspectives on neural underpinnings and adaptive benefits (and costs) of such diverse phenomena as spatial memory, colour vision, attention, spontaneous behaviour initiation, memory dynamics, relational rule learning and sleep, in a range of animals from marine invertebrates with exquisitely simple nervous systems to social insects forming societies with many thousands of individuals working together as a ‘superorganism’. This introduction provides context and history to tie the various approaches together, and concludes that there is an urgent need to understand the full neuron-to-neuron circuitry underlying various forms of information processing—not just to explore brain function comprehensively, but also to understand how (and how easily) cognitive capacities might evolve in the face of pertinent selection pressures. In the invertebrates...
Cyberinfrastructure integrates advanced computer, information, and communication technologies to empower computation-based and data-driven scientific practice and improve the synthesis and analysis of scientific data in a collaborative and shared fashion. As such, it now represents a paradigm shift in scientific research that has facilitated easy access to computational utilities and streamlined collaboration across distance and disciplines, thereby enabling scientific breakthroughs to be reached more quickly and efficiently. Spatial cyberinfrastructure seeks to resolve longstanding complex problems of handling and analyzing massive and heterogeneous spatial datasets as well as the necessity and benefits of sharing spatial data flexibly and securely. This article provides an overview and potential future directions of spatial cyberinfrastructure. The remaining four articles of the special feature are introduced and situated in the context of providing empirical examples of how spatial cyberinfrastructure is extending and enhancing scientific practice for improved synthesis and analysis of both physical and social science data. The primary focus of the articles is spatial analyses using distributed and high-performance computing, sensor networks...
This paper introduces a special feature on biodiversity conservation and poverty traps. We define and explain the core concepts and then identify four distinct classes of mechanisms that define important interlinkages between biodiversity and poverty. The multiplicity of candidate mechanisms underscores a major challenge in designing policy appropriate across settings. This framework is then used to introduce the ensuing set of papers, which empirically explore these various mechanisms linking poverty traps and biodiversity conservation.
Historical collapse of ancient states or civilizations has raised new awareness about its possible relevance to current issues of sustainability, in the context of global change. This Special Feature examines 12 case studies of societies under stress, of which seven suffered severe transformation. Outcomes were complex and unpredictable. Five others overcame breakdown through environmental, political, or socio-cultural resilience, which deserves as much attention as the identification of stressors. Response to environmental crises of the last millennium varied greatly according to place and time but drew from traditional knowledge to evaluate new information or experiment with increasing flexibility, even if modernization or intensification were decentralized and protracted. Longer-term diachronic experience offers insight into how societies have dealt with acute stress, a more instructive perspective for the future than is offered by apocalyptic scenarios.
Stable isotope ratio variations are regulated by physical and chemical laws. These rules depend on a relation with mass differences between isotopes. New classes of isotope variation effects that deviate from mass dependent laws, termed mass independent isotope effects, were discovered in 1983 and have a wide range of applications in basic chemistry and nature. In this special edition, new applications of these effects to physical chemistry, solar system origin models, terrestrial atmospheric and biogenic evolution, polar paleo climatology, snowball earth geology, and present day atmospheric sciences are presented.