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Complex Insight  - Understanding our world
Latest news on complex systems in life sciences, engineering, education and government
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MIT researchers find new MRI tool for drug discovery - Mass High Tech Business News

MIT researchers find new MRI tool for drug discovery - Mass High Tech Business News | Complex Insight  - Understanding our world | Scoop.it
Researchers at MIT’s Computer Science and Artificial Intelligence Laboratory have devised a new way to combine information from two different kinds of MRI scans, allowing drug developers to map which regions of the brain are affected by certain neurological disorders.

Neurological diseases, such as schizophrenia, are known to affect certain regions of the brain. Likewise, most drugs made to treat such diseases are made to act upon certain regions. The complication comes because those regions connect to other regions in way that no single brain scan can easily show. Polina Golland, an associate professor of computer science at MIT, has come up with an algorithm, or formula, which uses the information on the connections between them to map those regions. The algorithm is applied to two types of MRIs, both of which have been in use for at least 20 years: Diffusion MRIs, which look at the substance of the brain, as compared to functional MRIs, which look at brain activity. Golland said both types of scans are “very noisy,” and traditional analysis of them has focused on comparing hundreds of scans from different patients, rather than on extracting more information from different views of a single brain.. Click on the image or title to learn more.

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Smart cities to tackle migration issues

Smart cities to tackle migration issues | Complex Insight  - Understanding our world | Scoop.it

IBM chairman Samuel J Palmisano on Thursday said that India needs smarter cities and leaders to manage the large migration happening to its cities from rural towns. “The world will have 450 major metros by 2020. About 45 will be in India. There is large amount of migration happening to major Indian cities. About 30 people migrate to major Indian cities from rural areas every minute,” said Palmisano, at a function in Gurgaon to showcase IBM’s Smart City solutions.
Palmisano added that the number of people living in Indian cities will reach 843 million by 2050, which is more than the current combined population of the US, Brazil, Russia and Japan. “The problems of our major cities (in the world) are so severe that it becomes difficult for our leadership to manage them. Leaders have to be non-ideological if they have to get things done. The leaders of a smarter city think in terms of systems. They don’t confuse leadership with charisma or sound bites,” said Palmisano.  He went on to say that big data can help solve the world’s problems. “The information is already out there. You just have to do some predictive modelling and solve problems which face us every day.”. Click on image or title to learn more

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Striking image shows atomic bonds

Striking image shows atomic bonds | Complex Insight  - Understanding our world | Scoop.it

A pioneering team from IBM in Zurich  Switzerland show off images of the molecular world so detailed that the type of atomic bonds between their atoms can be discerned. The team, which included French and Spanish collaborators, used a variant of a technique called atomic force microscopy, or AFM. AFM uses a tiny metal tip passed over a surface, whose even tinier deflections are measured as the tip is scanned to and fro over a sample. The images show just how long the atomic bonds are, and the bright and dark spots correspond to higher and lower densities of electrons. Together, this information reveals just what kind of bonds they are - how many electrons pairs of atoms share - and what is going on chemically within the molecules. Click on the image or title to learn more.

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Who's Really Using Big Data

Who's Really Using Big Data | Complex Insight  - Understanding our world | Scoop.it

Interesting survey results on reality of big data adoption.A survey of executives at Fortune 1000 companies and large government agencies about where they stand on Big Data. Three high-level takeaways.First, the people we surveyed have high hopes for what they can get out of advanced analytics. Second, it's early days for most of them. They don't yet have the capabilities they need to exploit Big Data. Third, there are disconnects in the survey results — hints that the people inside individual organizations aren't aligned on some key issues.  Only 31% of IT respondents rank the "current role of Big Data" in their company as Planned or at Proof-of-Concept. CLick on the HBR image or the title for more info.

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How People Interact in Evolving Online Affiliation Networks

How People Interact in Evolving Online Affiliation Networks | Complex Insight  - Understanding our world | Scoop.it

The concept of social networks, in the age of Twitter and Facebook, seems like a really banal one. Social networks, however, have turned out to be a fertile ground for scientific studies of human interactions by not only social scientists, but also by physicists, from which we gain illuminating insights about ourselves and our societies. For example, why, and how, do we make new friends or establish fresh social ties? In this paper, we show that meaningful answers to these questions can be learned, by bringing concepts and methods from statistical physics to bear in a new analysis of the detailed growth dynamics of two networks associated with two online social-networking sites.

 

How People Interact in Evolving Online Affiliation Networks

Lazaros K. Gallos, Diego Rybski, Fredrik Liljeros, Shlomo Havlin, and Hernán A. Makse


Via Complexity Digest, Frédéric Amblard
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Boeing's 787 Dreamliner gets assembled quickly for Air India

Great catch by Jed Fisher. I have a big softspot for the 787. The shop floor instructions are created in some software developed by friends and former colleagues at SAP ( used to be Right Hemisphere where some of us used to work with Jed) and Chris and the team at Boeing Multimedia Seattle - created the groundcrew training simulator in our old Creator software.  Since there is a fairly good chance at some point various team and family members of the Complex Insight team will be on one of the Air India planes - this was just a nice reminder why its fun building software for hard problems  you get to work with great people on great projects. 


Via João Greno Brogueira, Jed Fisher
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The automatic chemist

The automatic chemist | Complex Insight  - Understanding our world | Scoop.it

Bartosz Grzybowski of Northwestern University in Illinois, US – who has already established himself as one of our most inventive chemists – has unveiled a ‘chemo-informatic’ scheme, Chematica, that can stake a reasonable claim to being paradigm-changing. Grzybowski and his colleagues have spent years assembling the transformations that link chemical species into a vast network that codifies and organises the known pathways through chemical space. The nodes of the network – molecules, elements and chemical reactions – are linked together by connecting reactants to products via the nexus of a known reaction. The full network contains around 7 million compound nodes and about the same number of reaction nodes. Grzybowski calls it a ‘collective chemical brain’.

 

The automatic chemist
Philip Ball

Chemistry World 22 August 2012

http://www.rsc.org/chemistryworld/2012/08/automatic-chemist


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Genomics: ENCODE explained : Nature : Nature Publishing Group

Genomics: ENCODE explained : Nature : Nature Publishing Group | Complex Insight  - Understanding our world | Scoop.it
The Encyclopedia of DNA Elements (ENCODE) project dishes up a hearty banquet of data that illuminate the roles of the functional elements of the human genome.

Via Gerd Moe-Behrens
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ncDNA and drift drive binding site accumulation - significant implications on synthetic biology

Ruths T, Nakhleh L.  

"The amount of transcription factor binding sites (TFBS) in an organism's genome positively correlates with the complexity of the regulatory network of the organism. However, the manner by which TFBS arise and accumulate in genomes and the effects of regulatory network complexity on the organism's fitness are far from being known. The availability of TFBS data from many organisms provides an opportunity to explore these issues, particularly from an evolutionary perspective.

RESULTS:
We analyzed TFBS data from five model organisms - E. coli K12, S. cerevisiae, C. elegans, D. melanogaster, A. thaliana - and found a positive correlation between the amount of non-coding DNA (ncDNA) in the organism's genome and regulatory complexity. Based on this finding, we hypothesize that the amount of ncDNA, combined with the population size, can explain the patterns of regulatory complexity across organisms. To test this hypothesis, we devised a genome-based regulatory pathway model and subjected it to the forces of evolution through population genetic simulations. The results support our hypothesis, showing neutral evolutionary forces alone can explain TFBS patterns, and that selection on the regulatory network function does not alter this finding.

CONCLUSIONS:
The cis-regulome is not a clean functional network crafted by adaptive forces alone, but instead a data source filled with the noise of non-adaptive forces. From a regulatory perspective, this evolutionary noise manifests as complexity on both the binding site and pathway level, which has significant implications on many directions in microbiology, genetics, and synthetic biology."

http://1.usa.gov/UjqZ5N


Via Gerd Moe-Behrens
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*Jay Keasling: 'We can use synthetic biology to make jet fuel'*

*Jay Keasling: 'We can use synthetic biology to make jet fuel'* | Complex Insight  - Understanding our world | Scoop.it

http://bit.ly/RbvfQR


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BSim - Agent based modeling tool for bacterial populations

BSim - Agent based modeling tool for bacterial populations | Complex Insight  - Understanding our world | Scoop.it

BSim is an agent-based modelling tool designed to allow for the study of bacterial populations. By enabling the description of bacterial behaviours, it attempts to provide an environment in which to investigate how local interactions between individual bacterium leads to the emergence of population level features, such as cooperation and synchronisation. For an good research example of how BSim is used see the paper here:

http://wwffm.org/2012/08/26/bsim-an-agent-based-tool-for-modeling-bacterial-populations-in-systems-and-synthetic-biology/

 

Click on the image or the title for more info.

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Drew Endy: Synthetic Biology

Drew Endy: Synthetic Biology | Complex Insight  - Understanding our world | Scoop.it

I first came across the work of Drew Endy and his team at MIT through a science comic they created to interest and explain synthetic biology to teenagers. This is a great short presentation (13 mins) he did at a Seed Magazine conference on Synthetic Biology and how with BioBricks we are starting to get standard components of synthetic biological mechanisms.. Worth watching. Click image or title for more.

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Mapping Mars with Open Planetary Data | MapBox

Mapping Mars with Open Planetary Data | MapBox | Complex Insight  - Understanding our world | Scoop.it

Curious where NASA's Curiosity is going? Then this is just he resource - a fantastic blog post from Mapbox.com on using open source mapping tools to create online maps of Mars. If you are into using map based services - this is a must read both for the technology covered, the processes described and because its awesome. Enjoy. Click on the image or the link to learn more.

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A Warning on Bank Complexity, From Someone Who Would Know

A Warning on Bank Complexity, From Someone Who Would Know | Complex Insight  - Understanding our world | Scoop.it

The interdependence and complexity of the global finanical system is is a rich area for complex systems research. So it is interesting when bank executives state who needs to own and manage the complexity of the system. Sallie L. Krawcheck, a former Bank of America and Citigroup executive, discussed her concerns about the complexity of financial behemoths at the Bloomberg Markets 50 Summit in Manhattan conference.“If you look at the job of the board, if you look at the job of investors, it’s the concern about complexity,”  When asked whether she saw evidence that banks had become too complex.

“It’s tough to generalize,” she said. “My concern is when the products themselves become too complex to understand, one begins to have a problem.” 

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The frailty of adaptive hypotheses for the origins of organismal complexity

The frailty of adaptive hypotheses for the origins of organismal complexity | Complex Insight  - Understanding our world | Scoop.it

"The vast majority of biologists engaged in evolutionary studies interpret virtually every aspect of biodiversity in adaptive terms", conversely Lynch proposes that "numerous aspects of genomic architecture, gene structure, and developmental pathways are difficult to explain without invoking the nonadaptive forces of genetic drift and mutation"

 

Source:

Lynch Michael

The frailty of adaptive hypotheses for the origins of organismal complexity.

PNAS May 15, 2007 vol. 104 no. Suppl 1 8597-8604


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BioBuilding: Synthetic Biology for Teachers: Lab 3 --TinkerCell - OpenWetWare

BioBuilding: Synthetic Biology for Teachers: Lab 3 --TinkerCell - OpenWetWare | Complex Insight  - Understanding our world | Scoop.it

As I have mentioned elsewhere I really like many of the ideas embedded in TinkerCell - Deepak Chandran did a great job in its design and implementation.  If you want to experiment with synthetic biology this is a great example for simulating a baterial photography system. Click on the image or title to learn more.

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Synthetic biology and social issues - Joyce Tait

Prof. Joyce Tait's presentation at the 4th New Phytologist Workshop (Synthetic Biology). More videos and information from the Workshop can be found at: http:...

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Microbial Cooperative Warfare

Cooperation among individuals of the same population directed against competing populations (cooperative warfare) is widespread in animals and plants. What happens in the microbial world is much less understood. Microbes can interact with one another through chemical signals, but little is known about the nature of their interactions, particularly outside the laboratory. On page 1228 of this issue, Cordero et al. (1) present a detailed analysis of ecological interaction networks, population structures, and genetic relatedness of microbes in the wild. They suggest that cooperative warfare is common in the microbial world.

 

Microbial Cooperative Warfare
Hélène Morlon

Science 7 September 2012:
Vol. 337 no. 6099 pp. 1184-1185
http://dx.doi.org/10.1126/science.1227512


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HPC allows UI cancer researchers to simulate tumor development | High Performance Computing

HPC allows UI cancer researchers to simulate tumor development | High Performance Computing | Complex Insight  - Understanding our world | Scoop.it

Uterine cancer is the fourth most common cancer among women, and the most common gynecological cancer. Researchers at the University of Iowa are using high-performance computing (HPC) to investigate how a tumor develops in normal uterine epithelium.

The majority of cancer research presumes that every cell in a tumor is driven by the same genetic alterations and follows same pathway to malignancy. Dr. Donghai Dai, associate professor of obstetrics and gynecology in the Carver College of Medicine, doesn’t think that’s the case. He believes the billions of cells that make up a tumor may each have their unique mutations that cause them to deviate from normal cell behavior. So, Dai and his team are taking a single-cell approach to studying the development of tumors. With complex mathematical models and the Helium computing cluster, administered by Information Technology Services, they can run simulations on millions of representative uterine cells each day. The researchers determine the fate of the cells through incorporation of the combined effect of numerous random mutations and varying hormonal stimulations. Click on the image or title to learn more.

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Hadoop Won't Displace Data Management Systems: Cloudera

ALways nice to here vendor CEO's state sense. In this article its Cloudera's CEO Mike Olson making sense. According to Olson, big data platform Hadoop will complement, not replace, legacy systems,. "Almost without exception, when we see Hadoop in real customer deployments, it's stood up next to existing infrastructure that's aimed at existing business problems," said Olson. He added, "In my view, it's unlikely that a brand-new entrant to the market is going to displace (legacy) tools for established workloads." Click on the title to learn more.

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The real reason for brains

The real reason for brains | Complex Insight  - Understanding our world | Scoop.it

From a talk  recorded on 13 July 2011. The BBC described this talk as "Neuroscientist Daniel Wolpert starts from a surprising premise: the brain evolved, not to think or feel, but to control movement". Anyone who has ever tried building autonomous real time robots - gets to understand this viewpoint pretty quickly.  Similarky anyone who spends a few minutes considering evolution - and what features need to first evolve to make species succesful - will know that tool use and intelligence are evolutionary side products of an animals need for spatial exploration in order to forage, hide and procreate not the other way around. The talk is both entertaining, data-rich and makes a lot of sense.  Worth watching. Click on the image or title of rmore info.

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Synthetic What? - Part 1: Conversations about Synthetic Biology.

A great scoop by SynBio team at Leukippos Institute: Designer, researchers and scientists Alexandra Daisy Ginsberg, Christina Agapakis and Patrick Boyle in conversation with Intel Futurist Brian David Johnson... 


Via Gerd Moe-Behrens
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New Device Can Measure the Mass of a Single Molecule

New Device Can Measure the Mass of a Single Molecule | Complex Insight  - Understanding our world | Scoop.it

Up until now, scientists could only calculate the mass of large groups of molecules, by ionizing them (giving them an electric charge) and then seeing how strongly they interacted with an electromagnetic field, a technique known as mass spectrometry. They had no way, however, of measuring the mass of a single molecule. This has now changed with Caltech scientists have created an ultra-sensitive device that can weigh an individual molecule for the first time.  By weighing each molecule, they were able to determine exactly which kind of IgM it was, hinting at potential future medical applications. The initial demonstration weighed a immunoglobulin M, or IgM molecule hinting at future medical applications. A kind of cancer known as Waldenström macroglobulinemia, for instance, is reflected by a particular ratio of IgM molecules in a patient’s blood, so future instruments building on this principle could monitor blood to detect antibody imbalances indicative of cancer. Click on the image or title to learn more.

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A model for development: biologists create first predictive computational model of gene networks

A model for development: biologists create first predictive computational model of gene networks | Complex Insight  - Understanding our world | Scoop.it

Caltech researchers built the first-ever computational model of the gene regulatory network controlling sea-urchin embryonic development. A small part of the network is shown here. Credit: Caltech/Davidson Lab The researchers described their computer model in a paper in the Proceedings of the National Academy of Sciences that appeared as an advance online publication on August 27. The model encompasses the gene regulatory network that controls the first 30 hours of the development of endomesoderm cells, which eventually form the embryo's gut, skeleton, muscles, and immune system. This network—so far the most extensively analyzed developmental gene regulatory network of any animal organism—consists of about 50 regulatory genes that turn one another on and off.

Read more at: http://phys.org/news/2012-08-biologists-gene-networks.html#jCp


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The Mom-and-Pop Water Shop from SEEDMAGAZINE.COM

The Mom-and-Pop Water Shop from SEEDMAGAZINE.COM | Complex Insight  - Understanding our world | Scoop.it

The UN says that each person needs between 20 and 50 liters of safe freshwater per day for drinking, cooking, and cleaning. Yet more than one in six people worldwide don’t have access to this amount—and some 2.5 billion live without access to even basic sanitation facilities. Combined, these have a shocking impact: Globally, diarrhea is the leading cause of illness and death. But the failure of international intervention has left the door open for grassroots solutions: In both Indonesia and the Philippines, a small entrepreneurial approach to safe water provision has achieved massive scale in an extremely short time span. The “water refill” industry, which utilizes low-cost technology to purify water on site in locally run businesses, has received little attention in the West, but it represents possibly the most effective means for water delivery in the developing world.Molecular biologist Ranjiv Khush and hydrologist Jeff Albert are now hoping to replicate the Asian model in other parts of the world, beginning in East Africa.  Click on the image or title to learn more.

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