Complexity at large


  • Carlos Gershenson


The following news item is taken in part from the May 7, 2010 issue of Science titled “A draft sequence of the Neandertal genome,” by Richard E. Green.

Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.

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The following news item is taken in part from the May 3, 2010 issue of Proceedings of National Academy of Science USA titled “Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks,” by Koon-Kiu Yan, Gang Fang, Nitin Bhardwaj, Roger P. Alexander, and Mark Gerstein.

The genome has often been called the operating system (OS) for a living organism. A computer OS is described by a regulatory control network termed the call graph, which is analogous to the transcriptional regulatory network in a cell. To apply our firsthand knowledge of the architecture of software systems to understand cellular design principles, we present a comparison between the transcriptional regulatory network of a well-studied bacterium (Escherichia coli) and the call graph of a canonical OS (Linux) in terms of topology and evolution. We show that both networks have a fundamentally hierarchical layout, but there is a key difference: ...

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The following news item is taken in part from the April 8, 2010 issue of PLoS Computer Biology titled “Dynamics and control of diseases in networks with community structure,” by Marcel Salathé and James H. Jones.

Here we use both data from social networking websites and computer generated networks to study the effect of community structure on epidemic spread. We find that community structure not only affects the dynamics of epidemics in networks, but that it also has implications for how networks can be protected from large-scale epidemics.

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The following news item is taken in part from the April 30, 2010 issue of Science titled “Biological systems theory,” by Jeremy Gunawardena.

Mathematical models are fashionable in systems biology, but there is a world of difference between a model and a theorem. When researchers build models, they make assumptions about a specific experimental setting and have to choose values for rate constants and other parameters. A theorem, by contrast, can apply to a setting of arbitrary molecular complexity, such as a biochemical network with many components. In a recent study, Shinar and Feinberg (1) formulate a theorem that shows when such biochemical networks exhibit “absolute concentration robustness.”

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The following news item is taken in part from the April 21, 2010 issue of arXiv titled “Diversity, competition, extinction: The ecophysics of language change,” by Ricard V. Solé, Bernat Corominas-Murtra, and Jordi Fortuny.

As early indicated by Charles Darwin, languages behave and change very much like living species. They display high diversity, differentiate in space and time, emerge and disappear. ... The models are reviewed here and include extinction, invasion, origination, spatial organization, coexistence and diversity as key concepts and are very simple in their defining rules. Such simplicity is used in order to catch the most fundamental laws of organization and those universal ingredients responsible for qualitative traits. The similarities between observed and predicted patterns indicate that an ecological theory of language is emerging, supporting (on a quantitative basis) its ecological nature, although key differences are also present.

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The following news item is taken in part from the April 24, 2010 issue of arXiv titled “Multi-scale modularity in complex networks,” by Renaud Lambiotte.

We focus on the detection of communities in multi-scale networks, namely networks made of different levels of organization and in which modules exist at different scales. It is first shown that methods based on modularity are not appropriate to uncover modules in empirical networks, mainly because modularity optimization has an intrinsic bias towards partitions having a characteristic number of modules which might not be compatible with the modular organization of the system. We argue for the use of more flexible quality functions incorporating a resolution parameter that allows us to reveal the natural scales of the system. Different types of multi-resolution quality functions are described and unified by looking at the partitioning problem from a dynamical viewpoint. Finally, significant values of the resolution parameter are selected by using complementary measures of robustness of the uncovered partitions. The methods are illustrated on a benchmark and an empirical network.

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The following news item is taken in part from the May 20, 2010 issue of Science titled “Creation of a bacterial cell controlled by a chemically synthesized genome,” by Daniel G. Gibson, John I. Glass, Carole Lartigue, Vladimir N. Noskov, Ray-Yuan Chuang, Mikkel A. Algire, Gwynedd A. Benders, Michael G. Montague, Li Ma, Monzia M. Moodie, Chuck Merryman, Sanjay Vashee, Radha Krishnakumar, Nacyra Assad-Garcia, Cynthia Andrews-Pfannkoch, Evgeniya A. Denisova, Lei Young, Zhi-Qing Qi, Thomas H. Segall-Shapiro, Christopher H. Calvey, Prashanth P. Parmar, Clyde A. Hutchison, III, Hamilton O. Smith, and J. Craig Venter.

We report the design, synthesis, and assembly of the 1.08-Mbp Mycoplasma mycoides JCVI-syn1.0 genome starting from digitized genome sequence information and its transplantation into a Mycoplasma capricolum recipient cell to create new Mycoplasma mycoides cells that are controlled only by the synthetic chromosome. The only DNA in the cells is the designed synthetic DNA sequence, including “watermark” sequences and other designed gene deletions and polymorphisms, and mutations acquired during the building process. The new cells have expected phenotypic properties and are capable of continuous self-replication.

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The following news item is taken in part from the May 2, 2010 issue of arXiv titled “The FuturIcT knowledge accelerator: Unleashing the power of information for a sustainable future,” by Dirk Helbing.

With our knowledge of the universe, we have sent men to the moon. We know microscopic details of objects around us and within us. And yet we know relatively little about how our society works and how it reacts to changes brought upon it. Humankind is now facing serious crises for which we must develop new ways to tackle the global challenges of humanity in the 21st century. With connectivity between people rapidly increasing, we are now able to exploit information and communication technologies to achieve major breakthroughs that go beyond the step-wise improvements in other areas. The need of a socio-economic knowledge collider was first pointed out in the OECD Global Science Forum on Applications of Complexity Science for Public Policy in Erice from October 5 to 7, 2008. Since then, many scientists have called for a large-scale ICT-based research initiative on techno-socialeconomic-environmental issues, sometimes phrased as a Manhattan-, Apollo-, or CERN-like project to study the way our living planet works in a social dimension. Due to the connotations, we use the term knowledge accelerator, here.

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The following news item is taken in part from the May 6, 2010 issue of Nature titled “Deciphering the splicing code,” by Yoseph Barash, John A. Calarco, Weijun Gao, Qun Pan, Xinchen Wang, Ofer Shai, Benjamin J. Blencowe, and Brendan J. Frey.

Alternative splicing has a crucial role in the generation of biological complexity, and its misregulation is often involved in human disease. Here we describe the assembly of a “splicing code,” which uses combinations of hundreds of RNA features to predict tissue-dependent changes in alternative splicing for thousands of exons. The code determines new classes of splicing patterns, identifies distinct regulatory programs in different tissues, and identifies mutation-verified regulatory sequences ...

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The following news item is taken in part from the May 13, 2010 issue of Nature titled “A formal test of the theory of universal common ancestry,” by Douglas L. Theobald.

Universal common ancestry (UCA) is a central pillar of modern evolutionary theory. As first suggested by Darwin, the theory of UCA posits that all extant terrestrial organisms share a common genetic heritage, each being the genealogical descendant of a single species from the distant past ... the model selection tests are found to overwhelmingly support UCA irrespective of the presence of horizontal gene transfer and symbiotic fusion events. These results provide powerful statistical evidence corroborating the monophyly of all known life.

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The following news item is taken in part from the March 10, 2010 issue of Swarm Intelligence titled “Principles and applications of swarm intelligence for adaptive routing in telecommunications networks,” by Frederick Ducatelle, Gianni A. Di Caro, and Luca M. Gambardella.

In the past few years, there has been much research on the application of swarm intelligence to the problem of adaptive routing in telecommunications networks. A large number of algorithms have been proposed for different types of networks, including wired networks and wireless ad hoc networks. In this paper, we give an overview of this research area. We address both the principles underlying the research and the practical applications that have been proposed.

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The following news item is taken in part from the May 14, 2010 issue of Science titled “Community structure in time-dependent, multiscale, and multiplex networks,” by Peter J. Mucha, Thomas Richardson, Kevin Macon, Mason A. Porter, and Jukka-Pekka Onnela.

Network science is an interdisciplinary endeavor, with methods and applications drawn from across the natural, social, and information sciences. A prominent problem in network science is the algorithmic detection of tightly connected groups of nodes known as communities. We developed a generalized framework of network quality functions that allowed us to study the community structure of arbitrary multislice networks, which are combinations of individual networks coupled through links that connect each node in one network slice to itself in other slices. This framework allows studies of community structure in a general setting encompassing networks that evolve over time, have multiple types of links (multiplexity), and have multiple scales.

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The following news item is taken in part from the May 13, 2010 issue of PLoS Computer Biology titled “Inductive game theory and the dynamics of animal conflict,” by Simon DeDeo, David C. Krakauer, and Jessica C. Flack.

Persistent conflict is one of the most important contemporary challenges to the integrity of society and to individual quality of life. Yet surprisingly little is understood about conflict. ... Here we develop a new method, Inductive Game Theory, and apply it to a time series gathered from detailed observation of a primate society. We are able to determine which types of behavior are most likely to generate periods of intense conflict, and we find that fights are not explained by single, aggressive individuals, but by complex interactions among groups of three or higher. Understanding how memory and strategy affect conflict dynamics is a crucial step towards designing better methods for prediction, management and control.

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The following news item is taken in part from the May 11, 2010 issue of Proceedings of National Academy of Science USA titled “The difference of being human: Morality,” by Francisco J. Ayala.

I raise the question of whether morality is biologically or culturally determined. The question of whether the moral sense is biologically determined may refer either to the capacity for ethics (i.e., the proclivity to judge human actions as either right or wrong), or to the moral norms accepted by human beings for guiding their actions. I propose that the capacity for ethics is a necessary attribute of human nature, whereas moral codes are products of cultural evolution.

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The following news item is taken in part from the June 1, 2010 issue of arXiv titled “Image information content characterization and classification by physical complexity,” by Hector Zenil, Jean-Paul Delahaye, and Cedric Gaucherel.

We present a method for estimating the complexity of an image based on the concept of logical depth. Unlike the application of the concept of algorithmic complexity by itself, the addition of the concept of logical depth results in a characterization of objects by organizational (physical) complexity. We use this measure to classify images by their information content. The method provides a means for evaluating and classifying objects by way of their visual representations.

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The following news item is taken in part from the May, 2010 issue of McKinsey Quaterly titled “Putting organizational complexity in its place,” by Julian Birkinshaw and Suzanne Heywood.

Not all complexity is bad for business—but executives don't always know what kind their company has. They should understand what creates complexity for most employees, remove what doesn't add value, and channel the rest to employees who can handle it effectively.

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The following news item is taken in part from the June 16, 2010 issue of Nature titled “Do metrics matter?,” by Alison Abbott, David Cyranoski, Nicola Jones, Brendan Maher, Quirin Schiermeier, and Richard Van Noorden.

No scientist's career can be summarized by a number. He or she spends countless hours troubleshooting experiments, guiding students and postdocs, writing or reviewing grants and papers, teaching, preparing for and organizing meetings, participating in collaborations, advising colleagues, serving on editorial boards and more—none of which is easily quantified. But when that scientist is seeking a job, promotion or even tenure, which of those duties will be rewarded? ...

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2nd Workshop on Complex Networks CompleNet 2010, Rio de Janeiro, Brazil, 2010/10/13-15 complenet

Business Complexity and the Global Leader Conference, Boston, MA, USA, 2010/10/17-20 Do metrics matter?

The 5th International Conference on Bio-Inspired Models of Network, Information and Computing Systems, Boston, MA, USA, 2010/12/1-3

IWSOS 2011, Fifth International Workshop on Self-Organizing Systems, Karlsruhe, Germany, 2011/02/23-25

IJCAI 2011, The 22nd International Joint Conference on Artificial Intelligence, Barcelona, Spain, 2011/07/19-22