Santa Fe Institute

About: Santa Fe Institute is a nonprofit organization based out in Santa Fe, New Mexico, United States. It is known for research contribution in the topics: Population & Complex network. The organization has 558 authors who have published 4558 publications receiving 396015 citations. The organization is also known as: SFI.

The role of recombination in the emergence of a complex and dynamic HIV epidemic

Abstract: Inter-subtype recombinants dominate the HIV epidemics in three geographical regions. To better understand the role of HIV recombinants in shaping the current HIV epidemic, we here present the results of a large-scale subtyping analysis of 9435 HIV-1 sequences that involve subtypes A, B, C, G, F and the epidemiologically important recombinants derived from three continents. The circulating recombinant form CRF02_AG, common in West Central Africa, appears to result from recombination events that occurred early in the divergence between subtypes A and G, followed by additional recent recombination events that contribute to the breakpoint pattern defining the current recombinant lineage. This finding also corrects a recent claim that G is a recombinant and a descendant of CRF02, which was suggested to be a pure subtype. The BC and BF recombinants in China and South America, respectively, are derived from recent recombination between contemporary parental lineages. Shared breakpoints in South America BF recombinants indicate that the HIV-1 epidemics in Argentina and Brazil are not independent. Therefore, the contemporary HIV-1 epidemic has recombinant lineages of both ancient and more recent origins. Taken together, we show that these recombinant lineages, which are highly prevalent in the current HIV epidemic, are a mixture of ancient and recent recombination. The HIV pandemic is moving towards having increasing complexity and higher prevalence of recombinant forms, sometimes existing as "families" of related forms. We find that the classification of some CRF designations need to be revised as a consequence of (1) an estimated > 5% error in the original subtype assignments deposited in the Los Alamos sequence database; (2) an increasing number of CRFs are defined while they do not readily fit into groupings for molecular epidemiology and vaccine design; and (3) a dynamic HIV epidemic context.

Statistical complexity of simple one-dimensional spin systems

Abstract: We present exact results for two complementary measures of spatial structure generated by one-dimensional spin systems with finite-range interactions. The first, excess entropy, measures the apparent spatial memory stored in configurations. The second, statistical complexity, measures the amount of memory needed to optimally predict the chain of spin values in configurations. These statistics capture distinct properties and are different from existing thermodynamic quantities.

Settlement scaling and increasing returns in an ancient society.

Abstract: A key property of modern cities is increasing returns to scale—the finding that many socioeconomic outputs increase more rapidly than their population size. Recent theoretical work proposes that this phenomenon is the result of general network effects typical of human social networks embedded in space and, thus, is not necessarily limited to modern settlements. We examine the extent to which increasing returns are apparent in archaeological settlement data from the pre-Hispanic Basin of Mexico. We review previous work on the quantitative relationship between population size and average settled area in this society and then present a general analysis of their patterns of monument construction and house sizes. Estimated scaling parameter values and residual statistics support the hypothesis that increasing returns to scale characterized various forms of socioeconomic production available in the archaeological record and are found to be consistent with key expectations from settlement scaling theory. As a consequence, these results provide evidence that the essential processes that lead to increasing returns in contemporary cities may have characterized human settlements throughout history, and demonstrate that increasing returns do not require modern forms of political or economic organization.