Inland waters have received only slight consideration in recent discussions of the global fisheries crisis, even though inland fisheries provide much-needed protein, jobs, and income, especially in poor rural communities of developing countries. Systematic overfishing of fresh waters is largely unrecognized because of weak reporting and because fishery declines take place within a complex of other pressures. Moreover, the ecosystem consequences of changes to the species, size, and trophic composition of fish assemblages are poorly understood. These complexities underlie the paradox that overexploitation of a fishery may not be marked by declines in total yield, even when individual species and long-term sustainability are highly threatened. Indeed, one of the symptoms of intense fishing in inland waters is the collapse of particular stocks even as overall fish production rises—a biodiversity crisis more than a fisheries crisis.

Ficus (Moraceae) is arguably one of the most important plant genera in lowland tropical rainforests. A brief review of tropical florulas also demonstrates that Ficus is the only ubiquitously diverse genus in lowland rainforests. Monoecious hemiepiphytic figs, constituting independent radiations in each tropical biome, make up a significant proportion of species everywhere, but in Asia dioecious figs have diversified into a variety of niches, making the assemblages of this region especially speciose. Pioneer attributes have endowed figs with tremendous evolutionary flexibility, while long-range seed dispersal ensures that a high proportion of the regional species pool is represented in local assemblages. Large numbers of Ficus species are able to coexist because many are extremely rare as a result of limited recruitment opportunities, which limits competition. They are nevertheless able to breed at low densities because they possess an efficient, long-range pollination system. These factors are likely to be important in the diversity of other plant groups in the tropics.

Complexity has recently risen to prominence in ecology as part of a broader interest that suggests its status is something more than just a scientific theory or property of reality. It may be helpful to consider complexity, and related terms such as “self-organization,” as recent metaphors deployed to advance knowledge on fundamental questions in ecology, including the relationship between parts and wholes, and between order and disorder. Though not commonly viewed as such, metaphors are an indispensable component of science, and should not be appraised as true or false, but rather in terms of how they help or hinder knowledge. By understanding metaphor as a necessary ally and not a threat to ecological knowledge, we may enrich our contextual understanding of complexity while continuing to invoke it in useful ways. The special section introduced by this article features essays by two prominent experts in ecology, complexity, and metaphor: science studies scholar Evelyn Fox Keller and theoretical ecologist Simon Levin.

My theme is the concept, and the term, “self-organization.” The history of this term, originally introduced by Immanuel Kant to characterize the unique properties of living organisms, is inseparable from the history of biology. Only in the second half of the 20th century does it begin to acquire the promise of a physicalistic understanding. This it does with two critical transformations in the meaning of the term: first, with the advent of cybernetics and its dissolution of the boundary between organisms and machines, and second, with the mathematical triumphs of nonlinear dynamical systems theory and accompanying claims to having dissolved the boundary between organisms and such physical phenomena as thunderstorms. How do these transformations affect the applicability of self-organization to the ecosystem—that provocatively hybrid entity that is part organism, part machine, and perhaps even part thunderstorm?

What explains the remarkable regularities in distribution and abundance of species, in size distributions of organisms, or in patterns of nutrient use? How does the biosphere maintain exactly the right conditions necessary for life as we know it? Gaia theory postulates that the biota regulates conditions at levels it needs for survival, but evolutionary biologists reject this explanation because it lacks a mechanistic basis. Similarly, the notion of self-organized criticality fails to recognize the importance of the heterogeneity and modularity of ecological systems. Ecosystems and the biosphere are complex adaptive systems, in which pattern emerges from, and feeds back to affect, the actions of adaptive individual agents, and in which cooperation and multicellularity can develop and provide the regulation of local environments, and indeed impose regularity at higher levels. The history of the biosphere is a history of coevolution between organisms and their environments, across multiple scales of space, time, and complexity.

We present evidence based on chemical analysis that identifies the scarlet dye produced by the scale insect Kermes echinatus as the shani (“red” in Hebrew) used toward the end of the second Holy Temple (AD 70). We know that this dye is produced by a coccoid species of scale. However, it is not yet known which of the coccoid species was used in the Holy Land in ancient times. Our results confirm the presence of the red pigment kermesic acid in K. echinatus extracts. The fact that K. echinatus is found in Israel suggests that the origin of the shani color mentioned in the Bible could have been local and that this dye was not an import from abroad, as most scholars have assumed. Our hypothesis, backed by our long-term observations, is supported by the color quality of kermesic acid, by the relative concentration of the pigment, and by the prevalence of K. echinatus in Israel.