Balinese "Water Temples" and the Management of Irrigation

Bali has figured prominently in debates on the question of whether irrigation centralizes state power. New evidence shows that irrigation is actually organized by networks of "water temples" that constitute an institutional system separate from the state. Earlier attempts to identify a discrete system of irrigation management misconceived the problem. For most crops, irrigation simply provides water for the plant's roots. But in a Balinese rice terrace, water is used to construct a complex, pulsed artificial ecosystem. Water temples manipulate the states of the system, at ascending levels in regional hierarchies. The permanence of water temple networks contrasts sharply with the instability of the traditional Balinese states. Since the water temples are real, perhaps it is the Balinese "state" that is chimerical.     

The Subak in Diaspora: Balinese Farmers and the Subak in South Sulawesi

The subak has a long history as an irrigators’ institution on Bali. It has also spread across Indonesia along with Balinese farmers who were resettled by colonial and post-colonial governments or who have migrated spontaneously since colonial times. While subaks have been much researched in Bali itself, little is known about subaks outside Bali. Luwu District in South Sulawesi is one of the areas where thousands of Balinese families settled in the last four decades. Based on research in this transmigration area, this paper analyzes the emergence and development of the subak in relation to the development of irrigation infrastructure of a state-built irrigation system. A comparison between two Balinese settlements in the same system shows that differences in infrastructural and managerial conditions and arrangements between parts of the irrigation system were major determinants of the institutional space allowed for the subak and ways in which the subaks developed.     

Dams and Dynasty,and the Colonial Transformation of Balinese Irrigation Management

This article takes issue with Stephen Lansing’s bottom-up model of Balinese irrigation management. Based on archival research and extensive fieldwork in the former south Balinese kingdom of Mengwi, it is argued that in pre-colonial days large scale irrigation depended largely on dynastic involvement. During the colonial period (1906–1942) the Dutch took over the role of regional irrigation management while they strengthened the autonomy of local irrigation associations.     

The anthropogenic environment lessens the intensity and prevalence of gastrointestinal parasites in Balinese long-tailed macaques (<Emphasis Type="Italic">Macaca fascicularis</Emphasis>)

The distribution of wildlife parasites in a landscape is intimately tied to the spatial distribution of hosts. In parasite species, including many gastrointestinal parasites, with obligate or common environmental life stages, the dynamics of the parasite can also be strongly affected by geophysical components of the environment. This is especially salient in host species, for example humans and macaques, which thrive across a wide variety of habitat types and quality and so are exposed to a wealth of environmentally resilient parasites. Here, we examine the effect of environmental and anthropogenic components of the landscape on the prevalence, intensity, and species diversity of gastrointestinal parasites across a metapopulation of long-tailed macaques on the island of Bali, Indonesia. Using principal-components analysis, we identified significant interaction effects between specific environmental and anthropogenic components of the landscape, parsing the Balinese landscape into anthropogenic (PC1), mixed environment (PC2), and non-anthropogenic (PC3) components. Further, we determined that the anthropogenic environment can mitigate the prevalence and intensity of specific gut parasites and the intensity of the overall community of gut parasites, but that non-anthropogenically driven landscape components have no significant effect in increasing or reducing the intensity or prevalence of the community of gut parasites in Balinese macaques.     

The Functional Role of Balinese Water Temples: A Response to Critics

In earlier publications we have proposed a model to explain the functional role of water temple networks in the agro-ecology of wet rice irrigation on the island of Bali. We argued that the key ecological effects of temple networks are best understood as emergent properties of a complex adaptive system. This argument implies that important aspects of the temple system are largely opaque from the perspective of conventional social science. We proposed that the Green Revolution created a real-world test of our model, by effectively removing the temple networks from their functional role in ecological management. The idea that water temple networks represent a hitherto-unknown kind of institution has been met with appropriate skepticism by other social scientists, who have run a fine-toothed comb through our evidence. Here we evaluate their critiques.     

TEMPLE AND KING: RESOURCE MANAGEMENT, RITUALS AND REDISTRIBUTION IN EARLY BALI

This article discusses the intricate relationship between economics, temples, rituals, and king and kingship in early Bali. So far the anthropological representation of the organization of the pre-colonial or early colonial Balinese state and society has oscillated between the 'theatre state' in which 'power served pomp' and the alleged disjunction of the state from an economy based for the most part on irrigated agriculture (rice). This article suggests that regional lords as well as kings had a substantial share in the economy as well as in the ritual organization of irrigation agriculture. This involvement functioned on both the local or regional level, with its corresponding irrigation associations ( subak ) and their rituals, and on the transregional level, with its major temples – which also acted as redistribution centres – and their authorities.     

Niche construction on Bali: the gods of the countryside

Human niche construction encompasses both purely biological phenomena, such as the evolution of lactose tolerance, and dual inheritance theory, which investigates the transmission of cultural information. But does niche construction help to explain phenomena in which conscious intention also plays a role? The creation of the engineered landscape of Balinese rice terraces offers a test case. Population genetic analysis and archaeological evidence are used to investigate whether this phenomenon emerged historically from trial and error by generations of farmers, or alternatively was designed by Bali''s rulers. In light of strong support for the former hypothesis, two models are developed to explore the emergence of functional structure at both local and global scales. As time goes forward and selected patterns of irrigation schedules are implemented, local variation in rice harvests influences future decisions by the farmers, creating a coupled human–natural system governed by feedback from the environment. This mathematical analysis received a measure of empirical support when government agricultural policies severed the local feedback channels, resulting in the almost instantaneous collapse of rice harvests. The historical process of niche construction may also have included an evolution of religious consciousness, reflected in the beliefs and practices of the water temple cult.     

Adaptive evolutionary walks require neutral intermediates in RNA fitness landscapes

In RNA fitness landscapes with interconnected networks of neutral mutations, neutral precursor mutations can play an important role in facilitating the accessibility of epistatic adaptive mutant combinations. I use an exhaustively surveyed fitness landscape model based on short sequence RNA genotypes (and their secondary structure phenotypes) to calculate the minimum rate at which mutants initially appearing as neutral are incorporated into an adaptive evolutionary walk. I show first, that incorporating neutral mutations significantly increases the number of point mutations in a given evolutionary walk when compared to estimates from previous adaptive walk models. Second, that incorporating neutral mutants into such a walk significantly increases the final fitness encountered on that walk - indeed evolutionary walks including neutral steps often reach the global optimum in this model. Third, and perhaps most importantly, evolutionary paths of this kind are often extremely winding in their nature and have the potential to undergo multiple mutations at a given sequence position within a single walk; the potential of these winding paths to mislead phylogenetic reconstruction is briefly considered.     

Outside Points of View in the Construction of Balinese Ethnicity and Religion

The ‘outside points of view’ of Muslims, Indian Hindus, tourists and other non‐Balinese towards Balinese culture and religion are often invoked by Balinese religious leaders and urban intelligentsia. This has been described in the literature as ‘defensiveness’ related to the process of gaining state acceptance for Balinese religion as Hinduism. I argue for a more subtle reading of the importance of assumed outside points of view to transformations of Balinese practices and to the construction of Balinese identities, by analysing examples from fieldwork (2001–2003) and from Balinese media relating to current debates over cockfighting, the Balinese language, and Balinese religion. One must differentiate the importance of outside points of view to differently positioned Balinese, determine what specific practices are called into question by such assumed points of view, and clearly distinguish between the flow of cultural categories and concepts in a globalised world and the phenomenon of perceived interactions between religions and cultures. Furthermore, a wider cross‐cultural perspective reveals the limitations of understanding these processes as uniquely postcolonial or postmodern.     

动物移动网络研究对景观生态学的贡献

景观生态学在其发展之初的20世纪80年代, 提出了关于景观网络研究(包括景观网络概念、网络结构指数和景观连接度)的基本构想, 这些构想需要在景观过程的研究中逐渐被落实和发展。动物移动过程因动物在斑块或廊道上有着独特丰富的属性特征、与周围资源环境之间存在复杂反馈而区别于无机物运移的景观过程, 则动物移动网络研究在实现关于景观网络研究的基本构想、推动景观生态学发展中贡献独特。因此, 总结动物移动网络研究的来源脉络及其对景观生态学的理论贡献对于景观网络领域和景观生态学学科的发展都具有重要意义。本文抓住景观生态学发展之初提出的关于景观网络研究的基本构想, 寻找和剖析其中所蕴含的景观生态学思想, 追踪这些思想如何被落实、发展、并形成目前的三个热点方向: 动物移动网络模拟、重要值评价和景观连接度分析; 总结这三个方向的研究进展, 指出整合动物的空间行为特征是必然发展趋势; 揭示出动物移动网络研究始终都以发掘斑块或廊道的动物有机体的属性特征(如种群数量)、以及描述这种属性在不同斑块或廊道之间的差异和联系为方向, 正是这种属性的发掘有效地落实、发展和丰富了关于景观网络研究的最初构想, 对景观生态学的贡献比其他过程更为独特。文章还总结了我国动物移动网络研究与国际研究相比较为滞后的现状, 指出其暂时尚未显示出对我国景观生态学的独特贡献; 强调发展源于跟踪定位数据的动物空间行为生态学研究是减小差距的重要、必要前提。期望本文能引发关于景观网络乃至景观生态学理论发展的方向性思考, 为研究者提供参考。     

Carnivores cross irrigation canals more often through overpasses than through culverts

As rainfall becomes scarcer or more erratic, we rely more on irrigation systems for agricultural and human water provision. Impacts of irrigation canals such as the barrier effect on wildlife movements are poorly documented. Although canal culverts and overpasses can be used by wildlife, little is known about their crossing behavior to guide barrier effect mitigation efforts. Over seven years, we recorded medium-sized carnivore crossings by video-surveillance through 30 culverts and 28 overpasses in a large irrigation project in south-central Portugal. We examined the influence of the structures’ features and landscape context on the likelihood of canal crossing. Culvert crossings were positively influenced by the proportion of nearby montado, a high nature value farming system. Overpass crossings were more likely in areas away from paved roads and with more nearby wetlands. Overpasses increased the crossing rates by about 11% relative to culverts and both were crossed more often in landscapes with evenly distributed land uses. In the project area, 20% of the montado has recently transitioned to irrigated agriculture, and wetlands have increased by 43%. It is therefore plausible that the increase in the crossing rate of overpasses relative to culverts will be accentuated. Our study produced the first evidence of a contrast in crossing rates among irrigation canal crossing structures. We have shown that the landscape can be a driver of animal crossings but irrigation projects can in turn be transformative of the landscape. Broadly, the fact that the deployment of irrigation canals may favor some land uses over others creates a conundrum that needs careful consideration when planning barrier effect mitigation interventions.     

Balinese Y-chromosome perspective on the peopling of Indonesia: genetic contributions from pre-neolithic hunter-gatherers, Austronesian farmers, and Indian traders

The island of Bali lies near the center of the southern chain of islands in the Indonesian archipelago, which served as a stepping-stone for early migrations of hunter-gatherers to Melanesia and Australia and for more recent migrations of Austronesian farmers from mainland Southeast Asia to the Pacific. Bali is the only Indonesian island with a population that currently practices the Hindu religion and preserves various other Indian cultural, linguistic, and artistic traditions (Lansing 1983). Here, we examine genetic variation on the Y chromosomes of 551 Balinese men to investigate the relative contributions of Austronesian farmers and pre-Neolithic hunter-gatherers to the contemporary Balinese paternal gene pool and to test the hypothesis of recent paternal gene flow from the Indian subcontinent. Seventy-one Y-chromosome binary polymorphisms (single nucleotide polymorphisms, SNPs) and 10 Y-chromosome-linked short tandem repeats (STRs) were genotyped on a sample of 1,989 Y chromosomes from 20 populations representing Indonesia (including Bali), southern China, Southeast Asia, South Asia, the Near East, and Oceania. SNP genotyping revealed 22 Balinese lineages, 3 of which (O-M95, O-M119, and O-M122) account for nearly 83.7% of Balinese Y chromosomes. Phylogeographic analyses suggest that all three major Y-chromosome haplogroups migrated to Bali with the arrival of Austronesian speakers; however, STR diversity patterns associated with these haplogroups are complex and may be explained by multiple waves of Austronesian expansion to Indonesia by different routes. Approximately 2.2% of contemporary Balinese Y chromosomes (i.e., K-M9*, K-M230, and M lineages) may represent the pre-Neolithic component of the Indonesian paternal gene pool. In contrast, eight other haplogroups (e.g., within H, J, L, and R), making up approximately 12% of the Balinese paternal gene pool, appear to have migrated to Bali from India. These results indicate that the Austronesian expansion had a profound effect on the composition of the Balinese paternal gene pool and that cultural transmission from India to Bali was accompanied by substantial levels of gene flow.     

Bazar,Big Kites and Other Boys' Things: Distinctions of Gender and Tradition in Balinese Youth Culture

Balinese society is undergoing rapid change, but remains discursively situated in a ‘timeless’ ethos of cultural tradition. This tension can be observed in relation to the cultural activities of the island's young people, particularly the young men. The staging of bazar (neighbourhood fundraising parties), the making of ogoh‐ogoh (giant papier‐mâché effigies to mark Nyepi, the Balinese New Year) and the competitive flying of oversize kites are–despite their sometimes contentious reception from older generations—popularly dubbed as ‘traditional’ expressions of Balinese youth culture. This recourse to tradition must be viewed in relation to two pervasive discourses: that of adat (customary law) and ajeg (a new protectionist ethos in the discourse on Balinese cultural identity). This paper argues that in contemporary urban Bali, male youth culture finds its most visible expressions in relation to the abiding standards of established public ritual and the equally abiding gender divisions that serve to guarantee the reproduction of ‘traditional’ social life. Rather than fighting aggressively against the grown‐up norm, these expressions replicate the public culture of the adult world—while drawing on global and national youth styles—and strive towards the expression of a specifically ‘Balinese’ youth culture.     

Towards a general theory of adaptive walks on rugged landscapes

Adaptive evolution, to a large extent, is a complex combinatorial optimization process. In this article we take beginning steps towards developing a general theory of adaptive "walks" via fitter variants in such optimization processes. We introduce the basic idea of a space of entities, each a 1-mutant neighbor of many other entities in the space, and the idea of a fitness ascribed to each entity. Adaptive walks proceed from an initial entity, via fitter neighbors, to locally or globally optimal entities that are fitter than their neighbors. We develop a general theory for the number of local optima, lengths of adaptive walks, and the number of alternative local optima accessible from any given initial entity, for the baseline case of an uncorrelated fitness landscape. Most fitness landscapes are correlated, however. Therefore we develop parts of a universal theory of adaptation on correlated landscapes by adaptive processes that have sufficient numbers of mutations per individual to "jump beyond" the correlation lengths in the underlying landscape. In addition, we explore the statistical character of adaptive walks in two independent complex combinatorial optimization problems, that of evolving a specific cell type in model genetic networks, and that of finding good solutions to the traveling salesman problem. Surprisingly, both show similar statistical features, encouraging the hope that a general theory for adaptive walks on correlated and uncorrelated landscapes can be found. In the final section we explore two limits to the efficacy of selection. The first is new, and surprising: for a wide class of systems, as the complexity of the entities under selection increases, the local optima that are attainable fall progressively closer to the mean properties of the underlying space of entities. This may imply that complex biological systems, such as genetic regulatory systems, are "close" to the mean properties of the ensemble of genomic regulatory systems explored by evolution. The second limit shows that with increasing complexity and a fixed mutation rate, selection often becomes unable to pull an adapting population to those local optima to which connected adaptive walks via fitter variants exist. These beginning steps in theory development are applied to maturation of the immune response, and to the problem of radiation and stasis. Despite the limitations of the adaptive landscape metaphor, we believe that further development along the lines begun here will prove useful.     

Plant diversity in a water-meadow landscape: the role of irrigation ditches

Species-rich, extensively managed grasslands are among the most threatened ecosystems in Europe. The traditional technique of meadow irrigation, formerly practised in large parts of Europe, may be a viable management option that meets both ecological and economical objectives. While studies on plant diversity of the meadow matrix exist, the role of other landscape components for biodiversity conservation is unknown. We quantify the role of irrigation and drainage ditches compared with field paths, and analysed the local and landscape plant species composition and diversity in a water-meadow landscape. The meadows are located in the river Queich catchment (Upper Rhine valley, Germany). We recorded plant species cover on 18 meadows, adjacent ditches and field paths and analysed alpha, beta and gamma diversity within and among these landscape components. Irrigation and drainage ditches were more species rich than meadows and more heterogeneous in their species composition compared with meadows and paths. Ditches contributed one-third of the landscape’s plant species numbers, habitat for wetland species and refuges for high nature value grassland species. Fertilization of the adjacent meadow had no negative impact on the ditch diversity, while well-maintained ditches were more plant species rich than ditches filled with sediments. Traditional flood meadow irrigation should be taken into account when sustainable grassland management techniques are discussed that meet economical and ecological needs. A major contribution to landscape richness arises from the ditch structures as crucial part of the traditional irrigation technique.     

Interactions matter—complexity in landscapes and ecosystems

In this review we argue that theories and methodology arising from the field of complex systems form a new paradigm for ecology. Patterns and processes resulting from interactions between individuals, populations, species and communities in landscapes are the core topic of ecology. These interactions form complex networks, which are the subject of intense research in complexity theory, informatics and statistical mechanics. This research has shown that complex natural networks often share common structures such as loops, trees and clusters. The observed structures contribute to widespread processes including feedback, non-linear dynamics, criticality and self-organisation. Simulation modelling is a key tool in studying complex networks and has become popular in ecology, especially in adaptive management. Important techniques include cellular automata and individual-based models. The complex systems paradigm has led to advances in landscape ecology, including a deeper understanding of the dynamics of spatial pattern formation, habitat fragmentation, epidemic processes, and genetic variation. Network analysis reveals that underlying patterns of interactions, such as small worlds and clusters, in food webs and ecosystems have strong implications for their stability and dynamics. These investigations illustrate how complexity theory and associated methodologies are transforming ecological research, providing new perspectives on old questions as well as raising many new ones.     

Synthetic shuffling and in vitro selection reveal the rugged adaptive fitness landscape of a kinase ribozyme

The relationship between genotype and phenotype is often described as an adaptive fitness landscape. In this study, we used a combination of recombination, in vitro selection, and comparative sequence analysis to characterize the fitness landscape of a previously isolated kinase ribozyme. Point mutations present in improved variants of this ribozyme were recombined in vitro in more than 10¹⁴ different arrangements using synthetic shuffling, and active variants were isolated by in vitro selection. Mutual information analysis of 65 recombinant ribozymes isolated in the selection revealed a rugged fitness landscape in which approximately one-third of the 91 pairs of positions analyzed showed evidence of correlation. Pairs of correlated positions overlapped to form densely connected networks, and groups of maximally connected nucleotides occurred significantly more often in these networks than they did in randomized control networks with the same number of links. The activity of the most efficient recombinant ribozyme isolated from the synthetically shuffled pool was 30-fold greater than that of any of the ribozymes used to build it, which indicates that synthetic shuffling can be a rich source of ribozyme variants with improved properties.     

Robustness to noise in gene expression evolves despite epistatic constraints in a model of gene networks

Stochastic noise in gene expression causes variation in the development of phenotypes, making such noise a potential target of stabilizing selection. Here, we develop a new simulation model of gene networks to study the adaptive landscape underlying the evolution of robustness to noise. We find that epistatic interactions between the determinants of the expression of a gene and its downstream effect impose significant constraints on evolution, but these interactions do allow the gradual evolution of increased robustness. Despite strong sign epistasis, adaptation rarely proceeds via deleterious intermediate steps, but instead occurs primarily through small beneficial mutations. A simple mathematical model captures the relevant features of the single‐gene fitness landscape and explains counterintuitive patterns, such as a correlation between the mean and standard deviation of phenotypes. In more complex networks, mutations in regulatory regions provide evolutionary pathways to increased robustness. These results chart the constraints and possibilities of adaptation to reduce expression noise and demonstrate the potential of a novel modeling framework for gene networks.     

Adaptive Landscape by Environment Interactions Dictate Evolutionary Dynamics in Models of Drug Resistance

The adaptive landscape analogy has found practical use in recent years, as many have explored how their understanding can inform therapeutic strategies that subvert the evolution of drug resistance. A major barrier to applications of these concepts is a lack of detail concerning how the environment affects adaptive landscape topography, and consequently, the outcome of drug treatment. Here we combine empirical data, evolutionary theory, and computer simulations towards dissecting adaptive landscape by environment interactions for the evolution of drug resistance in two dimensions—drug concentration and drug type. We do so by studying the resistance mediated by Plasmodium falciparum dihydrofolate reductase (DHFR) to two related inhibitors—pyrimethamine and cycloguanil—across a breadth of drug concentrations. We first examine whether the adaptive landscapes for the two drugs are consistent with common definitions of cross-resistance. We then reconstruct all accessible pathways across the landscape, observing how their structure changes with drug environment. We offer a mechanism for non-linearity in the topography of accessible pathways by calculating of the interaction between mutation effects and drug environment, which reveals rampant patterns of epistasis. We then simulate evolution in several different drug environments to observe how these individual mutation effects (and patterns of epistasis) influence paths taken at evolutionary “forks in the road” that dictate adaptive dynamics in silico. In doing so, we reveal how classic metrics like the IC₅₀ and minimal inhibitory concentration (MIC) are dubious proxies for understanding how evolution will occur across drug environments. We also consider how the findings reveal ambiguities in the cross-resistance concept, as subtle differences in adaptive landscape topography between otherwise equivalent drugs can drive drastically different evolutionary outcomes. Summarizing, we discuss the results with regards to their basic contribution to the study of empirical adaptive landscapes, and in terms of how they inform new models for the evolution of drug resistance.