Showing papers by "Santa Fe Institute published in 2008"

Hierarchical structure and the prediction of missing links in networks

Abstract: Networks have in recent years emerged as an invaluable tool for describing and quantifying complex systems in many branches of science. Recent studies suggest that networks often exhibit hierarchical organization, in which vertices divide into groups that further subdivide into groups of groups, and so forth over multiple scales. In many cases the groups are found to correspond to known functional units, such as ecological niches in food webs, modules in biochemical networks (protein interaction networks, metabolic networks or genetic regulatory networks) or communities in social networks. Here we present a general technique for inferring hierarchical structure from network data and show that the existence of hierarchy can simultaneously explain and quantitatively reproduce many commonly observed topological properties of networks, such as right-skewed degree distributions, high clustering coefficients and short path lengths. We further show that knowledge of hierarchical structure can be used to predict missing connections in partly known networks with high accuracy, and for more general network structures than competing techniques. Taken together, our results suggest that hierarchy is a central organizing principle of complex networks, capable of offering insight into many network phenomena.

Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection

Abstract: The precise identification of the HIV-1 envelope glycoprotein (Env) responsible for productive clinical infection could be instrumental in elucidating the molecular basis of HIV-1 transmission and in designing effective vaccines. Here, we developed a mathematical model of random viral evolution and, together with phylogenetic tree construction, used it to analyze 3,449 complete env sequences derived by single genome amplification from 102 subjects with acute HIV-1 (clade B) infection. Viral env genes evolving from individual transmitted or founder viruses generally exhibited a Poisson distribution of mutations and star-like phylogeny, which coalesced to an inferred consensus sequence at or near the estimated time of virus transmission. Overall, 78 of 102 subjects had evidence of productive clinical infection by a single virus, and 24 others had evidence of productive clinical infection by a minimum of two to five viruses. Phenotypic analysis of transmitted or early founder Envs revealed a consistent pattern of CCR5 dependence, masking of coreceptor binding regions, and equivalent or modestly enhanced resistance to the fusion inhibitor T1249 and broadly neutralizing antibodies compared with Envs from chronically infected subjects. Low multiplicity infection and limited viral evolution preceding peak viremia suggest a finite window of potential vulnerability of HIV-1 to vaccine-elicited immune responses, although phenotypic properties of transmitted Envs pose a formidable defense.

Parasites in food webs: the ultimate missing links

Abstract: Parasitism is the most common consumer strategy among organisms, yet only recently has there been a call for the inclusion of infectious disease agents in food webs. The value of this effort hinges on whether parasites affect food-web properties. Increasing evidence suggests that parasites have the potential to uniquely alter food-web topology in terms of chain length, connectance and robustness. In addition, parasites might affect food-web stability, interaction strength and energy flow. Food-web structure also affects infectious disease dynamics because parasites depend on the ecological networks in which they live. Empirically, incorporating parasites into food webs is straightforward. We may start with existing food webs and add parasites as nodes, or we may try to build food webs around systems for which we already have a good understanding of infectious processes. In the future, perhaps researchers will add parasites while they construct food webs. Less clear is how food-web theory can accommodate parasites. This is a deep and central problem in theoretical biology and applied mathematics. For instance, is representing parasites with complex life cycles as a single node equivalent to representing other species with ontogenetic niche shifts as a single node? Can parasitism fit into fundamental frameworks such as the niche model? Can we integrate infectious disease models into the emerging field of dynamic food-web modelling? Future progress will benefit from interdisciplinary collaborations between ecologists and infectious disease biologists.

Microbes on mountainsides: Contrasting elevational patterns of bacterial and plant diversity

Abstract: The study of elevational diversity gradients dates back to the foundation of biogeography. Although elevational patterns of plant and animal diversity have been studied for centuries, such patterns have not been reported for microorganisms and remain poorly understood. Here, in an effort to assess the generality of elevational diversity patterns, we examined soil bacterial and plant diversity along an elevation gradient. To gain insight into the forces that structure these patterns, we adopted a multifaceted approach to incorporate information about the structure, diversity, and spatial turnover of montane communities in a phylogenetic context. We found that observed patterns of plant and bacterial diversity were fundamentally different. While bacterial taxon richness and phylogenetic diversity decreased monotonically from the lowest to highest elevations, plants followed a unimodal pattern, with a peak in richness and phylogenetic diversity at mid-elevations. At all elevations bacterial communities had a tendency to be phylogenetically clustered, containing closely related taxa. In contrast, plant communities did not exhibit a uniform phylogenetic structure across the gradient: they became more overdispersed with increasing elevation, containing distantly related taxa. Finally, a metric of phylogenetic beta-diversity showed that bacterial lineages were not randomly distributed, but rather exhibited significant spatial structure across the gradient, whereas plant lineages did not exhibit a significant phylogenetic signal. Quantifying the influence of sample scale in intertaxonomic comparisons remains a challenge. Nevertheless, our findings suggest that the forces structuring microorganism and macroorganism communities along elevational gradients differ.

Policies Designed for Self-Interested Citizens May Undermine "The Moral Sentiments": Evidence from Economic Experiments

Abstract: High-performance organizations and economies work on the basis not only of material interests but also of Adam Smith's "moral sentiments." Well-designed laws and public policies can harness self-interest for the common good. However, incentives that appeal to self-interest may fail when they undermine the moral values that lead people to act altruistically or in other public-spirited ways. Behavioral experiments reviewed here suggest that economic incentives may be counterproductive when they signal that selfishness is an appropriate response; constitute a learning environment through which over time people come to adopt more self-interested motivations; compromise the individual's sense of self-determination and thereby degrade intrinsic motivations; or convey a message of distrust, disrespect, and unfair intent. Many of these unintended effects of incentives occur because people act not only to acquire economic goods and services but also to constitute themselves as dignified, autonomous, and moral individuals. Good organizational and institutional design can channel the material interests for the achievement of social goals while also enhancing the contribution of the moral sentiments to the same ends.

Leverage Cycles and the Anxious Economy

Abstract: ing opportunities for emerging economies. Their access to international markets has turned out to be very volatile, with frequent periods of market closures. Even worse, as we will show, emerging economies with sound fundamentals are the ones that issue less debt during these closures. The goal of this paper is to present a theory of asset pricing that will shed light on the problems of emerging assets (like emerging markets) that are not yet mature enough to be attractive to the general public. Their marginal buyers are liquidity constrained investors with small wealth relative to the whole economy, who are also marginal buyers of other risky assets. We will use our theory to argue that the periodic problems faced by emerging asset classes are sometimes symptoms of what we call a global anxious economy rather than of their own fundamental weaknesses.

Evolutionary emergence of responsive and unresponsive personalities

Abstract: In many animal species, individuals differ consistently in suites of correlated behaviors, comparable with human personalities. Increasing evidence suggests that one of the fundamental factors structuring personality differences is the responsiveness of individuals to environmental stimuli. Whereas some individuals tend to be highly responsive to such stimuli, others are unresponsive and show routine-like behaviors. Much research has focused on the proximate causes of these differences but little is known about their evolutionary origin. Here, we provide an evolutionary explanation. We develop a simple but general evolutionary model that is based on two key ingredients. First, the benefits of responsiveness are frequency-dependent; that is, being responsive is advantageous when rare but disadvantageous when common. This explains why responsive and unresponsive individuals can coexist within a population. Second, positive-feedback mechanisms reduce the costs of responsiveness; that is, responsiveness is less costly for individuals that have been responsive before. This explains why individuals differ consistently in their responsiveness, across contexts and over time. As a result, natural selection gives rise to stable individual differences in responsiveness. Whereas some individuals respond to environmental stimuli in all kinds of contexts, others consistently neglect such stimuli. Interestingly, such differences induce correlations among all kinds of other traits (e.g., boldness and aggressiveness), thus providing an explanation for environment-specific behavioral syndromes.

Inapparent infections and cholera dynamics

Abstract: In many infectious diseases, an unknown fraction of infections produce symptoms mild enough to go unrecorded, a fact that can seriously compromise the interpretation of epidemiological records This is true for cholera, a pandemic bacterial disease, where estimates of the ratio of asymptomatic to symptomatic infections have ranged from 3 to 100 (refs 1-5) In the absence of direct evidence, understanding of fundamental aspects of cholera transmission, immunology and control has been based on assumptions about this ratio and about the immunological consequences of inapparent infections Here we show that a model incorporating high asymptomatic ratio and rapidly waning immunity, with infection both from human and environmental sources, explains 50 yr of mortality data from 26 districts of Bengal, the pathogen's endemic home We find that the asymptomatic ratio in cholera is far higher than had been previously supposed and that the immunity derived from mild infections wanes much more rapidly than earlier analyses have indicated We find, too, that the environmental reservoir (free-living pathogen) is directly responsible for relatively few infections but that it may be critical to the disease's endemicity Our results demonstrate that inapparent infections can hold the key to interpreting the patterns of disease outbreaks New statistical methods, which allow rigorous maximum likelihood inference based on dynamical models incorporating multiple sources and outcomes of infection, seasonality, process noise, hidden variables and measurement error, make it possible to test more precise hypotheses and obtain unexpected results Our experience suggests that the confrontation of time-series data with mechanistic models is likely to revise our understanding of the ecology of many infectious diseases

Transparent and Catalytic Carbon Nanotube Films

Abstract: We report on the synthesis of thin, transparent, and highly catalytic carbon nanotube films. Nanotubes catalyze the reduction of triiodide, a reaction that is important for the dye-sensitized solar cell, with a charge-transfer resistance as measured by electrochemical impedance spectroscopy that decreases with increasing film thickness. Moreover, the catalytic activity can be significantly enhanced by exposing the nanotubes to ozone in order to introduce defects. Ozone-treated, defective nanotube films could serve as catalytic, transparent, and conducting electrodes for the dye-sensitized solar cell. Other possible applications include batteries, fuel cells, and electroanalytical devices.

The Coevolution of Cultural Groups and Ingroup Favoritism

Abstract: Cultural boundaries have often been the basis for discrimination, nationalism, religious wars, and genocide. Little is known, however, about how cultural groups form or the evolutionary forces behind group affiliation and ingroup favoritism. Hence, we examine these forces experimentally and show that arbitrary symbolic markers, though initially meaningless, evolve to play a key role in cultural group formation and ingroup favoritism because they enable a population of heterogeneous individuals to solve important coordination problems. This process requires that individuals differ in some critical but unobservable way and that their markers be freely and flexibly chosen. If these conditions are met, markers become accurate predictors of behavior. The resulting social environment includes strong incentives to bias interactions toward others with the same marker, and subjects accordingly show strong ingroup favoritism. When markers do not acquire meaning as accurate predictors of behavior, players show a markedly reduced taste for ingroup favoritism. Our results support the prominent evolutionary hypothesis that cultural processes can reshape the selective pressures facing individuals and so favor the evolution of behavioral traits not previously advantaged.

On a q-Central Limit Theorem Consistent with Nonextensive Statistical Mechanics

Abstract: The standard central limit theorem plays a fundamental role in Boltzmann-Gibbs statistical mechanics. This important physical theory has been generalized [1] in 1988 by using the entropy \(S_{q} = \frac{1-\sum_{i} p^{q}_{i}}{q-1}\)\(({\rm with}\,q\,\in {{{\mathcal{R}}}})\) instead of its particular BG case \(S_{1} = S_{BG} = - \sum_{i} p_{i}\,{\rm ln}\,p_{i}\). The theory which emerges is usually referred to as nonextensive statistical mechanics and recovers the standard theory for q = 1. During the last two decades, this q-generalized statistical mechanics has been successfully applied to a considerable amount of physically interesting complex phenomena. A conjecture[2] and numerical indications available in the literature have been, for a few years, suggesting the possibility of q-versions of the standard central limit theorem by allowing the random variables that are being summed to be strongly correlated in some special manner, the case q= 1 corresponding to standard probabilistic independence. This is what we prove in the present paper for \(1{\leqslant}\,q 0\), and normalizing constant Cq. These distributions, sometimes referred to as q-Gaussians, are known to make, under appropriate constraints, extremal the functional Sq (in its continuous version). Their q = 1 and q = 2 particular cases recover respectively Gaussian and Cauchy distributions.

Robustness of the European power grids under intentional attack.

Abstract: The power grid defines one of the most important technological networks of our times and sustains our complex society. It has evolved for more than a century into an extremely huge and seemingly robust and well understood system. But it becomes extremely fragile as well, when unexpected, usually minimal, failures turn into unknown dynamical behaviours leading, for example, to sudden and massive blackouts. Here we explore the fragility of the European power grid under the effect of selective node removal. A mean field analysis of fragility against attacks is presented together with the observed patterns. Deviations from the theoretical conditions for network percolation (and fragmentation) under attacks are analysed and correlated with non topological reliability measures.

Real Time Bayesian Estimation of the Epidemic Potential of Emerging Infectious Diseases

Abstract: Background Fast changes in human demographics worldwide, coupled with increased mobility, and modified land uses make the threat of emerging infectious diseases increasingly important. Currently there is worldwide alert for H5N1 avian influenza becoming as transmissible in humans as seasonal influenza, and potentially causing a pandemic of unprecedented proportions. Here we show how epidemiological surveillance data for emerging infectious diseases can be interpreted in real time to assess changes in transmissibility with quantified uncertainty, and to perform running time predictions of new cases and guide logistics allocations. Methodology/Principal Findings We develop an extension of standard epidemiological models, appropriate for emerging infectious diseases, that describes the probabilistic progression of case numbers due to the concurrent effects of (incipient) human transmission and multiple introductions from a reservoir. The model is cast in terms of surveillance observables and immediately suggests a simple graphical estimation procedure for the effective reproductive number R (mean number of cases generated by an infectious individual) of standard epidemics. For emerging infectious diseases, which typically show large relative case number fluctuations over time, we develop a Bayesian scheme for real time estimation of the probability distribution of the effective reproduction number and show how to use such inferences to formulate significance tests on future epidemiological observations. Conclusions/Significance Violations of these significance tests define statistical anomalies that may signal changes in the epidemiology of emerging diseases and should trigger further field investigation. We apply the methodology to case data from World Health Organization reports to place bounds on the current transmissibility of H5N1 influenza in humans and establish a statistical basis for monitoring its evolution in real time.

Information flows in causal networks

Abstract: We use a notion of causal independence based on intervention, which is a fundamental concept of the theory of causal networks, to define a measure for the strength of a causal effect. We call this measure "information flow" and compare it with known information flow measures such as transfer entropy.

Macroevolution of ecosystem engineering, niche construction and diversity

Abstract: Organisms influence their environments through activities that range from bioturbation to modification of redox gradients and construction of structures. Some of these activities modify the selective regime of the builder (niche construction) and some influence the ecological success of other species (ecosystem engineering) as well as their evolutionary prospects. In this article, I argue that these processes produce effects that persist over geological time, modulating macroevolutionary patterns and diversity. Examples include greater sediment bioturbation and increased thickness and persistence of shell beds. The impact of these processes has been increasing over time, with recent communities encompassing greater ecosystem engineering than those of the early Phanaerozoic. Thus, positive feedback through environmentally mediated selection seems to have increasingly enhanced biodiversity through the Phanaerozoic.

Linking Traits to Energetics and Population Dynamics to Predict Lizard Ranges in Changing Environments

Abstract: I present a dynamic bioenergetic model that couples individual energetics and population dynamics to predict current lizard ranges and those following climate warming. The model predictions are uniquely based on first principles of morphology, life history, and thermal physiology. I apply the model to five populations of a widespread North American lizard, Sceloporus undulatus, to examine how geographic variation in traits and life histories influences ranges. This geographic variation reflects the potential for species to adapt to environmental change. I then consider the range dynamics of the closely related Sceloporus graciosus. Comparing predicted ranges and actual current ranges reveals how dispersal limitations, species interactions, and habitat requirements influence the occupied portions of thermally suitable ranges. The dynamic model predicts individualistic responses to a uniform 3°C warming but a northward shift in the northern range boundary for all populations and species. In contra...

A general model for food web structure

Abstract: A central problem in ecology is determining the processes that shape the complex networks known as food webs formed by species and their feeding relationships. The topology of these networks is a major determinant of ecosystems' dynamics and is ultimately responsible for their responses to human impacts. Several simple models have been proposed for the intricate food webs observed in nature. We show that the three main models proposed so far fail to fully replicate the empirical data, and we develop a likelihood-based approach for the direct comparison of alternative models based on the full structure of the network. Results drive a new model that is able to generate all the empirical data sets and to do so with the highest likelihood.

What Happened to the Quants in August 2007?: Evidence from Factors and Transactions Data

Abstract: During the week of August 6, 2007, a number of quantitative long/short equity hedge funds experienced unprecedented losses. It has been hypothesized that a coordinated deleveraging of similarly constructed portfolios caused this temporary dislocation in the market. Using the simulated returns of long/short equity portfolios based on five specific valuation factors, we find evidence that the unwinding of these portfolios began in July 2007 and continued until the end of 2007. Using transactions data, we find that the simulated returns of a simple marketmaking strategy were significantly negative during the week of August 6, 2007, but positive before and after, suggesting that the Quant Meltdown of August 2007 was the combined effects of portfolio deleveraging throughout July and the first week of August, and a temporary withdrawal of marketmaking risk capital starting August 8th. Our simulations point to two unwinds - a mini-unwind on August 1st starting at 10:45am and ending at 11:30am, and a more sustained unwind starting at the open on August 6th and ending at 1:00pm - that began with stocks in the financial sector and long Book-to-Market and short Earnings Momentum. These conjectures have significant implications for the systemic risks posed by the hedge-fund industry.

Languages evolve in punctuational bursts

Abstract: Linguists speculate that human languages often evolve in rapid or punctuational bursts, sometimes associated with their emergence from other languages, but this phenomenon has never been demonstrated. We used vocabulary data from three of the world9s major language groups—Bantu, Indo-European, and Austronesian—to show that 10 to 33% of the overall vocabulary differences among these languages arose from rapid bursts of change associated with language-splitting events. Our findings identify a general tendency for increased rates of linguistic evolution in fledgling languages, perhaps arising from a linguistic founder effect or a desire to establish a distinct social identity.

The evolution of modularity in bacterial metabolic networks

Abstract: Deciphering the modular organization of metabolic networks and understanding how modularity evolves have attracted tremendous interest in recent years. Here, we present a comprehensive large scale characterization of modularity across the bacterial tree of life, systematically quantifying the modularity of the metabolic networks of >300 bacterial species. Three main determinants of metabolic network modularity are identified. First, network size is an important topological determinant of network modularity. Second, several environmental factors influence network modularity, with endosymbionts and mammal-specific pathogens having lower modularity scores than bacterial species that occupy a wider range of niches. Moreover, even among the pathogens, those that alternate between two distinct niches, such as insect and mammal, tend to have relatively high metabolic network modularity. Third, horizontal gene transfer is an important force that contributes significantly to metabolic modularity. We additionally reconstruct the metabolic network of ancestral bacterial species and examine the evolution of modularity across the tree of life. This reveals a trend of modularity decrease from ancestors to descendants that is likely the outcome of niche specialization and the incorporation of peripheral metabolic reactions.

Compilation and network analyses of cambrian food webs.

Abstract: A rich body of empirically grounded theory has developed about food webs—the networks of feeding relationships among species within habitats. However, detailed food-web data and analyses are lacking for ancient ecosystems, largely because of the low resolution of taxa coupled with uncertain and incomplete information about feeding interactions. These impediments appear insurmountable for most fossil assemblages; however, a few assemblages with excellent soft-body preservation across trophic levels are candidates for food-web data compilation and topological analysis. Here we present plausible, detailed food webs for the Chengjiang and Burgess Shale assemblages from the Cambrian Period. Analyses of degree distributions and other structural network properties, including sensitivity analyses of the effects of uncertainty associated with Cambrian diet designations, suggest that these early Paleozoic communities share remarkably similar topology with modern food webs. Observed regularities reflect a systematic dependence of structure on the numbers of taxa and links in a web. Most aspects of Cambrian food-web structure are well-characterized by a simple “niche model,” which was developed for modern food webs and takes into account this scale dependence. However, a few aspects of topology differ between the ancient and recent webs: longer path lengths between species and more species in feeding loops in the earlier Chengjiang web, and higher variability in the number of links per species for both Cambrian webs. Our results are relatively insensitive to the exclusion of low-certainty or random links. The many similarities between Cambrian and recent food webs point toward surprisingly strong and enduring constraints on the organization of complex feeding interactions among metazoan species. The few differences could reflect a transition to more strongly integrated and constrained trophic organization within ecosystems following the rapid diversification of species, body plans, and trophic roles during the Cambrian radiation. More research is needed to explore the generality of food-web structure through deep time and across habitats, especially to investigate potential mechanisms that could give rise to similar structure, as well as any differences.

Predictive information and explorative behavior of autonomous robots

Abstract: Measures of complexity are of immediate interest for the field of autonomous robots both as a means to classify the behavior and as an objective function for the autonomous development of robot behavior. In the present paper we consider predictive information in sensor space as a measure for the behavioral complexity of a two-wheel embodied robot moving in a rectangular arena with several obstacles. The mutual information (MI) between past and future sensor values is found empirically to have a maximum for a behavior which is both explorative and sensitive to the environment. This makes predictive information a prospective candidate as an objective function for the autonomous development of such behaviors. We derive theoretical expressions for the MI in order to obtain an explicit update rule for the gradient ascent dynamics. Interestingly, in the case of a linear or linearized model of the sensorimotor dynamics the structure of the learning rule derived depends only on the dynamical properties while the value of the MI influences only the learning rate. In this way the problem of the prohibitively large sampling times for information theoretic measures can be circumvented. This result can be generalized and may help to derive explicit learning rules from complexity theoretic measures.

Energy Uptake and Allocation During Ontogeny

Abstract: All organisms face the problem of how to fuel ontogenetic growth. We present a model, empirically grounded in data from birds and mammals, that correctly predicts how growing animals allocate food energy between synthesis of new biomass and maintenance of existing biomass. Previous energy budget models have typically had their bases in rates of either food consumption or metabolic energy expenditure. Our model provides a framework that reconciles these two approaches and highlights the fundamental principles that determine rates of food assimilation and rates of energy allocation to maintenance, biosynthesis, activity, and storage. The model predicts that growth and assimilation rates for all animals should cluster closely around two universal curves. Data for mammals and birds of diverse body sizes and taxa support these predictions.

Strong Reciprocity and the Roots of Human Morality

Abstract: Human morality is a key evolutionary adaptation on which human social behavior has been based since the Pleistocene era. Ethical behavior is constitutive of human nature, we argue, and human morality is as important an adaptation as human cognition and speech. Ethical behavior, we assert, need not be a means toward personal gain. Because of our nature as moral beings, humans take pleasure in acting ethically and are pained when acting unethically. From an evolutionary viewpoint, we argue that ethical behavior was fitness-enhancing in the years marking the emergence of Homo sapiens because human groups with many altruists fared better than groups of selfish individuals, and the fitness losses sustained by altruists were more than compensated by the superior performance of the groups in which they congregated.

The 1918–1919 influenza pandemic in England and Wales: spatial patterns in transmissibility and mortality impact

Abstract: Spatial variations in disease patterns of the 1918–1919 influenza pandemic remain poorly studied. We explored the association between influenza death rates, transmissibility and several geographical and demographic indicators for the autumn and winter waves of the 1918–1919 pandemic in cities, towns and rural areas of England and Wales. Average measures of transmissibility, estimated by the reproduction number, ranged between 1.3 and 1.9, depending on model assumptions and pandemic wave and showed little spatial variation. Death rates varied markedly with urbanization, with 30–40% higher rates in cities and towns compared with rural areas. In addition, death rates varied with population size across rural settings, where low population areas fared worse. By contrast, we found no association between transmissibility, death rates and indicators of population density and residential crowding. Further studies of the geographical mortality patterns associated with the 1918–1919 influenza pandemic may be useful for pandemic planning.

The Evolution and Distribution of Species Body Size

Abstract: The distribution of species body size within taxonomic groups exhibits a heavy right tail extending over many orders of magnitude, where most species are much larger than the smallest species. We provide a simple model of cladogenetic diffusion over evolutionary time that omits explicit mechanisms for interspecific competition and other microevolutionary processes, yet fully explains the shape of this distribution. We estimate the model's parameters from fossil data and find that it robustly reproduces the distribution of 4002 mammal species from the late Quaternary. The observed fit suggests that the asymmetric distribution arises from a fundamental trade-off between the short-term selective advantages (Cope's rule) and long-term selective risks of increased species body size in the presence of a taxon-specific lower limit on body size.