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Santa Fe Institute

NonprofitSanta Fe, New Mexico, United States
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.


Papers
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Journal ArticleDOI
TL;DR: It is proposed that signaling networks exploit noise at the single-cell level to increase population-level information transfer, allowing extracellular ligands, whose levels are also subject to noise, to incrementally regulate phenotypic changes.
Abstract: Signal transduction networks allow eukaryotic cells to make decisions based on information about intracellular state and the environment. Biochemical noise significantly diminishes the fidelity of signaling: networks examined to date seem to transmit less than 1 bit of information. It is unclear how networks that control critical cell-fate decisions (e.g., cell division and apoptosis) can function with such low levels of information transfer. Here, we use theory, experiments, and numerical analysis to demonstrate an inherent trade-off between the information transferred in individual cells and the information available to control population-level responses. Noise in receptor-mediated apoptosis reduces information transfer to approximately 1 bit at the single-cell level but allows 3–4 bits of information to be transmitted at the population level. For processes such as eukaryotic chemotaxis, in which single cells are the functional unit, we find high levels of information transmission at a single-cell level. Thus, low levels of information transfer are unlikely to represent a physical limit. Instead, we propose that signaling networks exploit noise at the single-cell level to increase population-level information transfer, allowing extracellular ligands, whose levels are also subject to noise, to incrementally regulate phenotypic changes. This is particularly critical for discrete changes in fate (e.g., life vs. death) for which the key variable is the fraction of cells engaged. Our findings provide a framework for rationalizing the high levels of noise in metazoan signaling networks and have implications for the development of drugs that target these networks in the treatment of cancer and other diseases.

108 citations

Journal ArticleDOI
TL;DR: Two approaches to automatically filter the changing configurations of spatial dynamical systems and extract coherent structures are presented, a modification of the local Lyapunov exponent approach suitable to cellular automata and other discrete spatial systems and a more traditional approach based on an order parameter and free energy is compared.
Abstract: Most current methods for identifying coherent structures in spatially extended systems rely on prior information about the form which those structures take. Here we present two approaches to automatically filter the changing configurations of spatial dynamical systems and extract coherent structures. One, local sensitivity filtering, is a modification of the local Lyapunov exponent approach suitable to cellular automata and other discrete spatial systems. The other, local statistical complexity filtering, calculates the amount of information needed for optimal prediction of the system's behavior in the vicinity of a given point. By examining the changing spatiotemporal distributions of these quantities, we can find the coherent structures in a variety of pattern-forming cellular automata, without needing to guess or postulate the form of that structure. We apply both filters to elementary and cyclical cellular automata (ECA and CCA) and find that they readily identify particles, domains, and other more complicated structures. We compare the results from ECA with earlier ones based upon the theory of formal languages and the results from CCA with a more traditional approach based on an order parameter and free energy. While sensitivity and statistical complexity are equally adept at uncovering structure, they are based on different system properties (dynamical and probabilistic, respectively) and provide complementary information.

108 citations

Journal ArticleDOI
TL;DR: The Theory Construction Methodology (TCM) as mentioned in this paper is a set of theoretical principles that putatively explain these phenomena, and the theory is used to construct a formal model, which is then used to evaluate the explanatory adequacy of the model by formalizing its empirical phenomena.
Abstract: This article aims to improve theory formation in psychology by developing a practical methodology for constructing explanatory theories: theory construction methodology (TCM). TCM is a sequence of five steps. First, the theorist identifies a domain of empirical phenomena that becomes the target of explanation. Second, the theorist constructs a prototheory, a set of theoretical principles that putatively explain these phenomena. Third, the prototheory is used to construct a formal model, a set of model equations that encode explanatory principles. Fourth, the theorist investigates the explanatory adequacy of the model by formalizing its empirical phenomena and assessing whether it indeed reproduces these phenomena. Fifth, the theorist studies the overall adequacy of the theory by evaluating whether the identified phenomena are indeed reproduced faithfully and whether the explanatory principles are sufficiently parsimonious and substantively plausible. We explain TCM with an example taken from research on intelligence (the mutualism model of intelligence), in which key elements of the method have been successfully implemented. We discuss the place of TCM in the larger scheme of scientific research and propose an outline for a university curriculum that can systematically educate psychologists in the process of theory formation.

107 citations

Journal ArticleDOI
TL;DR: In this paper, the authors compared the base-pairing probability distributions of 16 S and 16 S-like ribosomal RNAs of Archaea, Bacteria, chloroplasts, mitochondria and Eukarya, as predicted by the partition function approach for RNA folding.

107 citations

Journal ArticleDOI
TL;DR: Describing the DMFE for a collection of twenty single-nucleotide substitution mutants of Tobacco etch potyvirus across a set of eight host environments suggests that TEV may easily broaden its host range and improve fitness in new hosts, and that knowledge about theDMFE in the natural host does not allow for making predictions about its properties in an alternative host.
Abstract: Knowledge about the distribution of mutational fitness effects (DMFE) is essential for many evolutionary models. In recent years, the properties of the DMFE have been carefully described for some microorganisms. In most cases, however, this information has been obtained only for a single environment, and very few studies have explored the effect that environmental variation may have on the DMFE. Environmental effects are particularly relevant for the evolution of multi-host parasites and thus for the emergence of new pathogens. Here we characterize the DMFE for a collection of twenty single-nucleotide substitution mutants of Tobacco etch potyvirus (TEV) across a set of eight host environments. Five of these host species were naturally infected by TEV, all belonging to family Solanaceae, whereas the other three were partially susceptible hosts belonging to three other plant families. First, we found a significant virus genotype-by-host species interaction, which was sustained by differences in genetic variance for fitness and the pleiotropic effect of mutations among hosts. Second, we found that the DMFEs were markedly different between Solanaceae and non-Solanaceae hosts. Exposure of TEV genotypes to non-Solanaceae hosts led to a large reduction of mean viral fitness, while the variance remained constant and skewness increased towards the right tail. Within the Solanaceae hosts, the distribution contained an excess of deleterious mutations, whereas for the non-Solanaceae the fraction of beneficial mutations was significantly larger. All together, this result suggests that TEV may easily broaden its host range and improve fitness in new hosts, and that knowledge about the DMFE in the natural host does not allow for making predictions about its properties in an alternative host.

106 citations


Authors

Showing all 606 results

NameH-indexPapersCitations
James Hone127637108193
James H. Brown12542372040
Alan S. Perelson11863266767
Mark Newman117348168598
Bette T. Korber11739249526
Marten Scheffer11135073789
Peter F. Stadler10390156813
Sanjay Jain10388146880
Henrik Jeldtoft Jensen102128648138
Dirk Helbing10164256810
Oliver G. Pybus10044745313
Andrew P. Dobson9832244211
Carel P. van Schaik9432926908
Seth Lloyd9249050159
Andrew W. Lo8537851440
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Performance
Metrics
No. of papers from the Institution in previous years
YearPapers
202341
202241
2021297
2020309
2019263
2018231