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Genome Sizes and the Benford Distribution

Genome Sizes and the Benford Distribution | Papers | Scoop.it

Simply by assuming that the (protein) coding and non-coding fractions of the genome must have different dynamics and that the non-coding fraction must be particularly versatile and therefore be controlled by a variety of (unspecified) probability distribution functions (pdf’s), we are able to predict that the number of ORFs for Eukaryotes follows a Benford distribution and must therefore have a specific logarithmic form. Using the data for the 1000+ genomes available to us in early 2010, we find that the Benford distribution provides excellent fits to the data over several orders of magnitude.

 

Friar JL, Goldman T, Pérez–Mercader J (2012) Genome Sizes and the Benford Distribution. PLoS ONE 7(5): e36624. http://dx.doi.org/doi:10.1371/journal.pone.0036624

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Safecracking the Brain

Safecracking the Brain | Papers | Scoop.it

It’s hard to imagine an encryption machine more sophisticated than the human brain. This three-pound blob of tissue holds an estimated 86 billion neurons, cells that rapidly fire electrical pulses in split-second response to whatever stimuli our bodies encounter in the external environment. Each neuron, in turn, has thousands of spindly branches that reach out to nodes, called synapses, which transmit those electrical messages to other cells. Somehow the brain interprets this impossibly noisy code, allowing us to effectively respond to an ever-changing world.

Given the complexity of the neural code, it’s not surprising that some neuroscientists are borrowing tricks from more experienced hackers: cryptographers, the puzzle-obsessed who draw on math, logic, and computer science to make and break secret codes.


http://nautil.us/issue/20/creativity/safecracking-the-brain-rp

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How Network Science Is Changing Our Understanding of Law

How Network Science Is Changing Our Understanding of Law | Papers | Scoop.it
The first network analysis of the entire body of European Community legislation reveals the pattern of links between laws and their resilience to change.
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luiy's curator insight, Today, 3:14 AM

One of the more fascinating areas of science that has emerged in recent years is the study of networks and their application to everyday life. It turns out that many important properties of our world are governed by networks with very specific properties.

 

These networks are not random by any means. Instead, they are often connected in the now famous small world pattern in which any part of the network can be reached in a relatively small number of steps. These kinds of networks lie behind many natural phenomena such as earthquakes, epidemics and forest fires and are equally ubiquitous in social phenomena such as the spread of fashions, languages, and even wars.

 

So it should come as no surprise that the same kind of network should exist in the legal world. Today, Marios Koniaris and pals at the National Technical University of Athens in Greece show that the network of links between laws follows exactly the same pattern. They say their network approach provides a unique insight into the nature of the law, the way it has emerged and how changes may influence it in the future.

 

Suggested by Walter Quattrociocchi
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Structural Patterns of the Occupy Movement on Facebook

Structural Patterns of the Occupy Movement on Facebook | Papers | Scoop.it

In this work we study a peculiar example of social organization on Facebook: the Occupy Movement -- i.e., an international protest movement against social and economic inequality organized online at a city level. We consider 179 US Facebook public pages during the time period between September 2011 and February 2013. The dataset includes 618K active users and 753K posts that received about 5.2M likes and 1.1M comments. By labeling user according to their interaction patterns on pages -- e.g., a user is considered to be polarized if she has at least the 95% of her likes on a specific page -- we find that activities are not locally coordinated by geographically close pages, but are driven by pages linked to major US cities that act as hubs within the various groups. Such a pattern is verified even by extracting the backbone structure -- i.e., filtering statistically relevant weight heterogeneities -- for both the pages-reshares and the pages-common users networks.


Structural Patterns of the Occupy Movement on Facebook
Michela Del Vicario, Qian Zhang, Alessandro Bessi, Fabiana Zollo, Antonio Scala, Guido Caldarelli, Walter Quattrociocchi

http://arxiv.org/abs/1501.07203

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luiy's curator insight, Today, 3:51 AM
Data Description The dataset represents a complete screenshot of the Occupy Movement in the period immediately following the outbreak of the protest on September 17th, 2011 in the Zuccotti Park of New York. The dataset covers all the posts until the end of February 2013, at the time when all the major protests were no more active. After the Zuccotti occupation, in fact, an October full of similar occupational events followed, leading to an international protest movement that extended itself until the end of 2012, when the movement was principally an online collective protest.
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Synchronization as Aggregation: Cluster Kinetics of Pulse-Coupled Oscillators

We consider models of identical pulse-coupled oscillators with global interactions. Previous work showed that under certain conditions such systems always end up in sync, but did not quantify how small clusters of synchronized oscillators progressively coalesce into larger ones. Using tools from the study of aggregation phenomena, we obtain exact results for the time-dependent distribution of cluster sizes as the system evolves from disorder to synchrony.


Synchronization as Aggregation: Cluster Kinetics of Pulse-Coupled Oscillators
Kevin P. O'Keeffe, Pavel L. Krapivsky, Steven H. Strogatz

http://arxiv.org/abs/1501.04115

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Expectations of brilliance underlie gender distributions across academic disciplines

The gender imbalance in STEM subjects dominates current debates about women’s underrepresentation in academia. However, women are well represented at the Ph.D. level in some sciences and poorly represented in some humanities (e.g., in 2011, 54% of U.S. Ph.D.’s in molecular biology were women versus only 31% in philosophy). We hypothesize that, across the academic spectrum, women are underrepresented in fields whose practitioners believe that raw, innate talent is the main requirement for success, because women are stereotyped as not possessing such talent. This hypothesis extends to African Americans’ underrepresentation as well, as this group is subject to similar stereotypes. Results from a nationwide survey of academics support our hypothesis (termed the field-specific ability beliefs hypothesis) over three competing hypotheses.


Expectations of brilliance underlie gender distributions across academic disciplines
Sarah-Jane Leslie, Andrei Cimpian, Meredith Meyer, Edward Freeland

Science 16 January 2015:
Vol. 347 no. 6219 pp. 262-265
http://dx.doi.org/10.1126/science.1261375 

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Degeneracy: Demystifying and destigmatizing a core concept in systems biology

Often relegated to the methods section of genetic research articles, the term “degeneracy” is regularly misunderstood and its theoretical significance widely understated. Degeneracy describes the ability of different structures to be conditionally interchangeable in their contribution to system functions. Frequently mislabeled redundancy, degeneracy refers to structural variation whereas redundancy refers to structural duplication. Sources of degeneracy include, but are not limited to, (1) duplicate structures that differentiate yet remain isofunctional, (2) unrelated isofunctional structures that are dispersed endogenously or exogenously, (3) variable arrangements of interacting structures that achieve the same output through multiple pathways, and (4) parcellation of a structure into subunits that can still variably perform the same initial function. The ability to perform the same function by drawing upon an array of dissimilar structures contributes advantageously to the integrity of a system. Drawing attention to the heterogeneous construction of living systems by highlighting the concept of degeneracy valuably enhances the ways scientists think about self-organization, robustness, and complexity. Labels in science, however, can sometimes be misleading. In scientific nomenclature, the word “degeneracy” has calamitous proximity to the word “degeneration” used by pathologists and the shunned theory of degeneration once promoted by eugenicists. This article disentangles the concept of degeneracy from its close etymological siblings and offers a brief overview of the historical and contemporary understandings of degeneracy in science. Distinguishing the importance of degeneracy will hopefully allow systems theorists to more strategically operationally conceptualize the distributed intersecting networks that comprise complex living systems.


Degeneracy: Demystifying and destigmatizing a core concept in systems biology
Paul H. Mason

Complexity
Volume 20, Issue 3, pages 12–21, January/February 2015

http://dx.doi.org/10.1002/cplx.21534 

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On optimal modularity for system construction

Modularity is a natural instrument and a ubiquitous practice for the engineering of human-made systems. However, modularization remains more of an art than a science; to the extent that the notion of optimal modularity is rarely used in engineering design. We prove that optimal modularity exists (at least for construction)—and is achieved through balanced modularization as structural symmetry in the distribution of the sizes of modules. We show that system construction cost is highly sensitive to both the number of modules and the modularization structure. However, this sensitivity has an inverse relationship with process capability and is minimal for highly capable construction processes with small process uncertainties. Conclusions are reached by a Bayesian estimation technique for a relatively simple construction model originally introduced by Herbert Simon for the hypothetical production of a linear structure, taking into account errors that may occur in the work associated with the production of the links between the nodes in the structure for varied numbers of modules.


On optimal modularity for system construction
Mahmoud Efatmaneshnik and Michael j Ryan
http://dx.doi.org/10.1002/cplx.21646

Complexity, Early View

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Saberes Sin Fronteras Ong's curator insight, January 23, 5:44 PM

#modularización #sistema

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Where Next for Microbiome Research?

The development of high-throughput sequencing technologies has transformed our capacity to investigate the composition and dynamics of the microbial communities that populate diverse habitats. Over the past decade, these advances have yielded an avalanche of metagenomic data. The current stage of “van Leeuwenhoek”–like cataloguing, as well as functional analyses, will likely accelerate as DNA and RNA sequencing, plus protein and metabolic profiling capacities and computational tools, continue to improve. However, it is time to consider: what’s next for microbiome research? The short pieces included here briefly consider the challenges and opportunities awaiting microbiome research.


Waldor MK, Tyson G, Borenstein E, Ochman H, Moeller A, et al. (2015) Where Next for Microbiome Research? PLoS Biol 13(1): e1002050. http://dx.doi.org/10.1371/journal.pbio.1002050 ;

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NETWORKED MINDS: Where human evolution is heading

Having studied the technological and social forces shaping our societies, we are now turning to the evolutionary forces. Among the millions of species on earth, humans are truly unique. 
What is the recipe of our success? What makes us special? How do we decide? How will we further evolve? What will our role be, when algorithms, computers, machines, and robots are getting ever more powerful? How will our societies change?


http://futurict.blogspot.ie/2014/12/networked-minds-where-human-evolution.html

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Estimating Food Consumption and Poverty Indices with Mobile Phone Data

Recent studies have shown the value of mobile phone data to tackle problems related to economic development and humanitarian action. In this research, we assess the suitability of indicators derived from mobile phone data as a proxy for food security indicators. We compare the measures extracted from call detail records and airtime credit purchases to the results of a nationwide household survey conducted at the same time. Results show high correlations (> .8) between mobile phone data derived indicators and several relevant food security variables such as expenditure on food or vegetable consumption. This correspondence suggests that, in the future, proxies derived from mobile phone data could be used to provide valuable up-to-date operational information on food security throughout low and middle income countries.


Estimating Food Consumption and Poverty Indices with Mobile Phone Data
Adeline Decuyper, Alex Rutherford, Amit Wadhwa, Jean-Martin Bauer, Gautier Krings, Thoralf Gutierrez, Vincent D. Blondel, Miguel A. Luengo-Oroz

http://arxiv.org/abs/1412.2595

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SOCIAL FORCES: Revealing the causes of success or disaster

SOCIAL FORCES: Revealing the causes of success or disaster | Papers | Scoop.it

We have seen that self-organizing systems can be very effective and efficient, but their macro-level behavior crucially depends on the interaction rules, interaction strength, and institutional settings. To get things right, it's important to understand the factors that drive the dynamics of the system. 


http://futurict.blogspot.ie/2014/12/social-forces-revealing-causes-of.html

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Computational fact checking from knowledge networks

Traditional fact checking by expert journalists cannot keep up with the enormous volume of information that is now generated online. Computational fact checking may significantly enhance our ability to evaluate the veracity of dubious information. Here we show that the complexities of human fact checking can be approximated quite well by finding the shortest path between concept nodes under properly defined semantic proximity metrics on knowledge graphs. Framed as a network problem this approach is feasible with efficient computational techniques. We evaluate this approach by examining tens of thousands of claims related to history, entertainment, geography, and biographical information using a public knowledge graph extracted from Wikipedia. Statements independently known to be true consistently receive higher support via our method than do false ones. These findings represent a significant step toward scalable computational fact-checking methods that may one day mitigate the spread of harmful misinformation.


Computational fact checking from knowledge networks
Giovanni Luca Ciampaglia, Prashant Shiralkar, Luis M. Rocha, Johan Bollen, Filippo Menczer, Alessandro Flammini

http://arxiv.org/abs/1501.03471

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Comparative analysis of existing models for power-grid synchronization

Comparative analysis of existing models for power-grid synchronization | Papers | Scoop.it

The dynamics of power-grid networks is becoming an increasingly active area of research within the physics and network science communities. The results from such studies are typically insightful and illustrative, but are often based on simplifying assumptions that can be either difficult to assess or not fully justified for realistic applications. Here we perform a comprehensive comparative analysis of three leading models recently used to study synchronization dynamics in power-grid networks—a fundamental problem of practical significance given that frequency synchronization of all power generators in the same interconnection is a necessary condition for a power grid to operate. We show that each of these models can be derived from first principles within a common framework based on the classical model of a generator, thereby clarifying all assumptions involved. This framework allows us to view power grids as complex networks of coupled second-order phase oscillators with both forcing and damping terms. Using simple illustrative examples, test systems, and real power-grid datasets, we study the inherent frequencies of the oscillators as well as their coupling structure, comparing across the different models. We demonstrate, in particular, that if the network structure is not homogeneous, generators with identical parameters need to be modeled as non-identical oscillators in general. We also discuss an approach to estimate the required (dynamical) system parameters that are unavailable in typical power-grid datasets, their use for computing the constants of each of the three models, and an open-source MATLAB toolbox that we provide for these computations.


Comparative analysis of existing models for power-grid synchronization,
Takashi Nishikawa and Adilson E Motter,
New J. Phys. 17, 015012 (2015)

http://dx.doi.org/10.1088/1367-2630/17/1/015012 ;

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Determinants of Meme Popularity

Online social media have greatly affected the way in which we communicate with each other. However, little is known about what are the fundamental mechanisms driving dynamical information flow in online social systems. Here, we introduce a generative model for online sharing behavior and analytically show, using techniques from mathematical population genetics, that competition between memes for the limited resource of user attention leads to a type of self-organized criticality, with heavy-tailed distributions of meme popularity: a few memes "go viral" but the majority become only moderately popular. The time-dependent solutions of the model are shown to fit empirical micro-blogging data on hashtag usage, and to predict novel scaling features of the data. The presented framework, in contrast to purely empirical studies or simulation-based models, clearly distinguishes the roles of two distinct factors affecting meme popularity: the memory time of users and the connectivity structure of the social network.


Determinants of Meme Popularity
James P. Gleeson, Kevin P. O'Sullivan, Raquel A. Baños, Yamir Moreno

http://arxiv.org/abs/1501.05956

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luiy's curator insight, Today, 3:30 AM

In summary, despite its simplicity, the model matches the empirical popularity distribution of hashtags on Twitter remarkably well; this is consistent with random-copying models of human decision-making [28] where the quality of the product—here, the “interestingness” of the meme—is less important than the social influence of peers’ decisions[29]. The generalization of the model (as shown in the SM) to incorporate (i) heterogeneous user activity rates and (ii) a joint distribution p jk of the number of users followed j and the number of followers k, remains analytically tractable and confirms the robustness of our main finding: that competition between memes for the limited resource of user attention induces criticality in the vanis hing-innovation limit, giving power-law popularity distributions and epochs of linear-in-time popularity growth. We believe that theanalytical results and potential for fast fitting to data will render this a useful null model for further investigations of the entangled effects of memory, network structure, and competition on information spread through social networks [30].

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Everyday the Same Picture: Popularity and Content Diversity

Everyday the Same Picture: Popularity and Content Diversity | Papers | Scoop.it

Facebook is flooded by diverse and heterogeneous content, from kittens up to music and news, passing through satirical and funny stories. Each piece of that corpus reflects the heterogeneity of the underlying social background. In the Italian Facebook we have found an interesting case: a page having more than 40K followers that every day posts the same picture of Toto Cutugno, a popular Italian singer. In this work, we use such a page as a benchmark to study and model the effects of content heterogeneity on popularity. In particular, we use that page for a comparative analysis of information consumption patterns with respect to pages posting science and conspiracy news. In total, we analyze about 2M likes and 190K comments, made by approximately 340K and 65K users, respectively. We conclude the paper by introducing a model mimicking users selection preferences accounting for the heterogeneity of contents.


Everyday the Same Picture: Popularity and Content Diversity
Alessandro Bessi, Fabiana Zollo, Michela Del Vicario, Antonio Scala, Guido Caldarelli, Fabio Petroni, Bruno Gonçalves, Walter Quattrociocchi

http://arxiv.org/abs/1501.07201

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Ricci Curvature of the Internet Topology

Analysis of Internet topologies has shown that the Internet topology has negative curvature, measured by Gromov's "thin triangle condition", which is tightly related to core congestion and route reliability. In this work we analyze the discrete Ricci curvature of the Internet, defined by Ollivier, Lin, etc. Ricci curvature measures whether local distances diverge or converge. It is a more local measure which allows us to understand the distribution of curvatures in the network. We show by various Internet data sets that the distribution of Ricci cuvature is spread out, suggesting the network topology to be non-homogenous. We also show that the Ricci curvature has interesting connections to both local measures such as node degree and clustering coefficient, global measures such as betweenness centrality and network connectivity, as well as auxilary attributes such as geographical distances. These observations add to the richness of geometric structures in complex network theory.


Ricci Curvature of the Internet Topology
Chien-Chun Ni, Yu-Yao Lin, Jie Gao, Xianfeng David Gu, Emil Saucan

http://arxiv.org/abs/1501.04138

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The Big World of Nanothermodynamics

Nanothermodynamics extends standard thermodynamics to facilitate finite-size effects on the scale of nanometers. A key ingredient is Hill’s subdivision potential that accommodates the non-extensive energy of independent small systems, similar to how Gibbs’ chemical potential accommodates distinct particles. Nanothermodynamics is essential for characterizing the thermal equilibrium distribution of independently relaxing regions inside bulk samples, as is found for the primary response of most materials using various experimental techniques. The subdivision potential ensures strict adherence to the laws of thermodynamics: total energy is conserved by including an instantaneous contribution from the entropy of local configurations, and total entropy remains maximized by coupling to a thermal bath. A unique feature of nanothermodynamics is the completely-open nanocanonical ensemble. Another feature is that particles within each region become statistically indistinguishable, which avoids non-extensive entropy, and mimics quantum-mechanical behavior. Applied to mean-field theory, nanothermodynamics gives a heterogeneous distribution of regions that yields stretched-exponential relaxation and super-Arrhenius activation. Applied to Monte Carlo simulations, there is a nonlinear correction to Boltzmann’s factor that improves agreement between the Ising model and measured non-classical critical scaling in magnetic materials. Nanothermodynamics also provides a fundamental mechanism for the 1/f noise found in many materials.


The Big World of Nanothermodynamics
Ralph V. Chamberlin

Entropy 2015, 17(1), 52-73; http://dx.doi.org/10.3390/e17010052

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Cognition and behavior

An important question in the debate over embodied, enactive, and extended cognition has been what has been meant by “cognition”. What is this cognition that is supposed to be embodied, enactive, or extended? Rather than undertake a frontal assault on this question, however, this paper will take a different approach. In particular, we may ask how cognition is supposed to be related to behavior. First, we could ask whether cognition is supposed to be (a type of) behavior. Second, we could ask whether we should attempt to understand cognitive processes in terms of antecedently understood cognitive behaviors. This paper will survey some of the answers that have been (implicitly or explicitly) given in the embodied, enactive, and extended cognition literature, then suggest reasons to believe that we should answer both questions in the negative.


Cognition and behavior
Ken Aizawa

Synthese
January 2015

http://dx.doi.org/10.1007/s11229-014-0645-5 ;

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All in the (bigger) family

The next time you are about to dig into a freshly steamed lobster for dinner, think “cockroach,” or better yet, “dragonfly.” A decade of genetic data and other evidence has persuaded most researchers that insects and crustaceans, long considered widely separated branches of the arthropod family tree, actually belong together. Now they are exploring the consequences of the revision, which traces insect ancestry to certain crustaceans. “When I think about traits in insects, I now have a context for where they came from,” says Jon Harrison, an evolutionary physiologist at Arizona State University, Tempe, who has spent 25 years investigating insect respiration. “It's a total change.”


All in the (bigger) family
Elizabeth Pennisi

Science 16 January 2015:
Vol. 347 no. 6219 pp. 220-221
http://dx.doi.org/10.1126/science.347.6219.220 

Complexity Digest's insight:

Let us hope that this revision promotes insectivorism: http://go.ted.com/suG 

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Development, information and social connectivity in Côte d'Ivoire

Understanding human socioeconomic development has proven to be one of the most difficult and persistent problems in science and policy. Traditional policy has often attempted to promote human development through infrastructure and the delivery of services, but the link between these engineered systems and the complexity of human socioeconomic behavior remains poorly understood. Recent research suggests that the key to socioeconomic progress lies in the development of processes whereby new information is created by individuals and organizations and embedded in the structure of social networks at a diverse set of scales, from nations to cities to firms. Here, we formalize these ideas in terms of network theory—namely the spatial network of mobile phone communications in Côte d’Ivoire--to show how incipient socioeconomic connectivity may constitute a general obstacle to development. Inspired by recent progress in the theory of cities as complex systems, we then propose a set of tests for these theories using telecommunications network data and describe how telecommunication services may generally help promote socioeconomic development.


Development, information and social connectivity in Côte d’Ivoire
Clio Andris and Luis MA Bettencourt

Infrastructure Complexity 2014, 1:1  http://dx.doi.org/10.1186/s40551-014-0001-4

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Human-Data Interaction: The Human Face of the Data-Driven Society

The increasing generation and collection of personal data has created a complex ecosystem, often collaborative but sometimes combative, around companies and individuals engaging in the use of these data. We propose that the interactions between these agents warrants a new topic of study: Human-Data Interaction (HDI). In this paper we discuss how HDI sits at the intersection of various disciplines, including computer science, statistics, sociology, psychology and behavioural economics. We expose the challenges that HDI raises, organised into three core themes of legibility, agency and negotiability, and we present the HDI agenda to open up a dialogue amongst interested parties in the personal and big data ecosystems.


Human-Data Interaction: The Human Face of the Data-Driven Society
Richard Mortier, Hamed Haddadi, Tristan Henderson, Derek McAuley, Jon Crowcroft

http://arxiv.org/abs/1412.6159

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A Unifying Theory for Scaling Laws of Human Populations

The spatial distribution of people exhibits clustering across a wide range of scales, from household to continental  scales. Empirical data indicates simple power-law scalings for the size distribution of cities (known as Zipf's law), the geographic distribution of friends, and the population density fluctuations as a function of scale. We derive a simple statistical model that explains all of these scaling laws based on a single unifying principle involving the random spatial growth of clusters of people on all scales. The model makes important new predictions for the spread of diseases and other social phenomena.


A Unifying Theory for Scaling Laws of Human Populations
Henry W. Lin, Abraham Loeb

http://arxiv.org/abs/1501.00738

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Why It’s Good To Be Wrong

Why It’s Good To Be Wrong | Papers | Scoop.it

That human beings can be mistaken in anything they think or do is a proposition known as fallibilism. Stated abstractly like that, it is seldom contradicted. Yet few people have ever seriously believed it, either.

That our senses often fail us is a truism; and our self-critical culture has long ago made us familiar with the fact that we can make mistakes of reasoning too. But the type of fallibility that I want to discuss here would be all-pervasive even if our senses were as sharp as the Hubble Telescope and our minds were as logical as a computer. It arises from the way in which our ideas about reality connect with reality itself—how, in other words, we can create knowledge, and how we can fail to.

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The multilayer temporal network of public transport in Great Britain

The multilayer temporal network of public transport in Great Britain | Papers | Scoop.it

Despite the widespread availability of information concerning public transport coming from different sources, it is extremely hard to have a complete picture, in particular at a national scale. Here, we integrate timetable data obtained from the United Kingdom open-data program together with timetables of domestic flights, and obtain a comprehensive snapshot of the temporal characteristics of the whole UK public transport system for a week in October 2010. In order to focus on multi-modal aspects of the system, we use a coarse graining procedure and define explicitly the coupling between different transport modes such as connections at airports, ferry docks, rail, metro, coach and bus stations. The resulting weighted, directed, temporal and multilayer network is provided in simple, commonly used formats, ensuring easy access and the possibility of a straightforward use of old or specifically developed methods on this new and extensive dataset.


The multilayer temporal network of public transport in Great Britain
Riccardo Gallotti & Marc Barthelemy

Scientific Data, Published online: 6 January 2015; | http://dx.doi.org/10.1038/sdata.2014.56

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