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Latest news on complex systems in life sciences, engineering, education and government
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Transcriptic Aims to Make the Biology Lab Programmable - Bio-IT World

Transcriptic Aims to Make the Biology Lab Programmable - Bio-IT World | Complex Insight  - Understanding our world | Scoop.it
Bio-IT World
Transcriptic Aims to Make the Biology Lab Programmable
Bio-IT World
At a time when monkeys are exerting telepathic control over mechanical limbs, most biologists still don't have access to robotics for even the simplest procedures.
ComplexInsight's insight:

Transcriptic is an awesomely promising start up - that aims to provide automated execution of different lab protocols.  Intersting article at Bio-IT World. If you are interested in the future of weblab work and how it connects to synthetic biology and bio discovery - well worth reading.

 

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Canada to give WHO Ebola vaccine

Canada to give WHO Ebola vaccine | Complex Insight  - Understanding our world | Scoop.it

Following the WHO decision that it was ethical to use untested drugs on Ebola patients if it gave them a possibility of recovery, Canada says it will donate up to 1,000 doses of an experimental Ebola vaccine to help battle the disease's outbreak in West Africa.

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Dinosaurs shrank for 50 million years to become birds - life - 31 July 2014 - New Scientist

Dinosaurs shrank for 50 million years to become birds - life - 31 July 2014 - New Scientist | Complex Insight  - Understanding our world | Scoop.it
The meat-eating theropod dinosaurs shrank 12 times in a row, going from over 200 kilograms to less than a kilogram, until they were small enough to fly
ComplexInsight's insight:

Evidence in a study by  Mike Lee of the South Australian Museum in Adelaide and colleagues has shown that a gradual wave of evolution led theropods to evolve into modern birds. Great article from New Scientist on Mike Lee's research work.

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A World Cup Visitor: Polio from Africa in Brazil | Science Blogs | WIRED

A World Cup Visitor: Polio from Africa in Brazil | Science Blogs | WIRED | Complex Insight  - Understanding our world | Scoop.it
The World Health Organization announced on Monday that a polio sample was collected in March at Viracopos International Airport in Campinas, which is about 60 miles outside Sao Paulo, and is where many of the World Cup teams have been landing. The agency said no cases of polio have been identified and there is no evidence the disease has been transmitted.
ComplexInsight's insight:

Another awesome article by Maryn Mckenna, highlighting the interconnectedness of our health ecossystem as polio virus from Afric is found in a Brazilian sewer. The possible vector - visitors for the world cup. Article very worth reading.

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Cellular traffic control system mapped for the first time

Cellular traffic control system mapped for the first time | Complex Insight  - Understanding our world | Scoop.it

Cells regulate the uptake of nutrients and messenger cargos and their transport within the cell. This process is known as endocytosis and membrane traffic. Different cargos dock onto substrate specific receptors on the cell membrane. Special proteins such as kinases, GTPases and coats, activate specific entry routes and trigger the uptake of the receptors into the cell. For their uptake, the receptors and docked cargos become enclosed by the cell membrane. In the next steps, the membrane invaginates and becomes constricted. The resulting vesicle is guided via several distinct stations, cellular organelles, to its final destination in the cell.

 

For her study, Dr. Prisca Liberali, senior scientist in the team of Professor Lucas Pelkmans, sequentially switched off 1200 human genes. Using automated high-throughput light microscopy and computer vision, she could monitor and compare 13 distinct transport paths involving distinct receptors and cellular organelles. Precise quantifications of thousands of single cells identified the genes required for the different transport routes. Surprisingly, sets of transport routes are co-regulated and coordinated in specific ways by different programs of regulatory control.

 

Subsequently, Dr. Liberali calculated the hierarchical order within the genetic network and thereby identified the regulatory topology of cellular transport. "The transport into the cell and within the cells proceeds analogously to the cargo transport within a city" describes the scientist. "Like in a city, the traffic on the routes within a cell and their intersections is tightly regulated by traffic lights and signs to guide the cargo flow."

 

Thanks to this unique quantitative map, the fine regulatory details of transport paths and processes within a cells could be mapped for the first time. Particularly the genes that encode for these traffic lights and switches are often de-regulated in disease. With this map, it is now possible to predict how this leads to traffic jams in the cells, causing the disease phenotype. Alternatively, since many drugs have been developed to target these traffic lights and switches, the map can be used to come up with possible drug combinations to target unwanted traffic, such as viruses, to the waste disposal system of the cell.


Via Dr. Stefan Gruenwald, burkesquires
ComplexInsight's insight:

Mapping the fine regulatory details of transport paths and processes within cells is key to understanding gene and protein functions, cancer, viral interactions and potential treatments.  Interesting read.

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VIZBIplus - Visualizing the Future of Biomedicine

VIZBIplus - Visualizing the Future of Biomedicine | Complex Insight  - Understanding our world | Scoop.it
Community Resource for the VIZBI conference series on computer methods for visualizing biological data, including genomes, protein sequences, phylogenies, macromolecular structures, systems biology, microscopy, and magnetic resonance imaging.
ComplexInsight's insight:

If you are fortunate enough to be in Sidney on the 29th of May this is a must not miss event. David Goodsells illustrations have inspired a generation of scientists and artists, His watercoloured biological illustrations directly influenced some of the leading biomedical animators including Drew Berry and team and helped fire imaginations and understanding of molecular machinery. Really hoping VIVID sydney record this and make the recording available at a later date. Pure Awesome.

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The Gigaom interview: Why synthetic biology and the Netflix model are the future of medicine

The Gigaom interview: Why synthetic biology and the Netflix model are the future of medicine | Complex Insight  - Understanding our world | Scoop.it
Life is a programming language, and molecular biologist Andrew Hessel thinks that it will be increasingly available to anyone interested in designing with the building blocks of life.
ComplexInsight's insight:

Good article on Autodesk's Project Cyborg and update from some of the research coming out of Autodesk's Bio/Nano research group.

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WHO | WHO’s first global report on antibiotic resistance reveals serious, worldwide threat to public health

New WHO report provides the most comprehensive picture of antibiotic resistance to date, with data from 114 countries
ComplexInsight's insight:

Resistance to antibiotics poses a "major global threat" to public health, says a new report by the World Health Organization (WHO).

The WHO team analysed data from 114 countries and said resistance was happening now "in every region of the world". The report describes a "post-antibiotic era", where people die from simple infections that have been treatable for decades.

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Ancient Fossils Suggest Complex Life Evolved on Land | Simons Foundation

Ancient Fossils Suggest Complex Life Evolved on Land | Simons Foundation | Complex Insight  - Understanding our world | Scoop.it
Evidence from Southwestern deserts suggests that oxygen-breathing organisms arose on land rather than in the seas.
ComplexInsight's insight:

Understanding prehistoric evolution is at best a game of educated guesses. Paul Knuath's research has helped revolutionize our perspective of possible evolutionary pathways and this is a great article putting that research in perspective.

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FANTOM

FANTOM | Complex Insight  - Understanding our world | Scoop.it
ComplexInsight's insight:

In our bodies every cell contains the same genetic code, however the active or expressed genes determine cell function.  Which genes are expressed is controlled by tiny bits of the genome called promoters and enhancers and different cell types are determined by different combinations of promoters and enhancers. Now an international consortium of researchers known as FANTOM, led by the RIKEN institute in Japan have created the  clearest map yet of how genes control cells to make our bodies function. The map is already challenging ideas about what our genes do and how they interact and may accelerate the development of gene-based therapies. The team examined more than 800 human tissue samples, covering nearly all cell types, and  found 44,000 enhancers and 180,000 promoters that control gene expression.

 

 

 

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Towards a Methodology for Validation of Centrality Measures in Complex Networks

Towards a Methodology for Validation of Centrality Measures in Complex Networks | Complex Insight  - Understanding our world | Scoop.it

Our empirical analysis demonstrates that in the chosen network data sets, nodes which had a high Closeness Centrality also had a high Eccentricity Centrality. Likewise high Degree Centrality also correlated closely with a high Eigenvector Centrality. Whereas Betweenness Centrality varied according to network topology and did not demonstrate any noticeable pattern. In terms of identification of key nodes, we discovered that as compared with other centrality measures, Eigenvector and Eccentricity Centralities were better able to identify important nodes.

 

Batool K, Niazi MA (2014) Towards a Methodology for Validation of Centrality Measures in Complex Networks. PLoS ONE 9(4): e90283. http://dx.doi.org/10.1371/journal.pone.0090283


Via Complexity Digest
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Liz Rykert's curator insight, April 15, 2014 10:50 PM

Love this stuff.

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Twins’ immune systems look like those of complete strangers

Twins’ immune systems look like those of complete strangers | Complex Insight  - Understanding our world | Scoop.it
When it comes to our immune response, genetics takes a back seat to pathogens.
ComplexInsight's insight:

Our adaptive immune system, the one that responds to specific pathogens, relies on T cells and B cells. These cells make proteins that have a key job: distinguish between the harmless proteins in all of our cells and foreign proteins that may be harmful. In T cells, these molecules are creatively called T cell receptors (TCRs), and in B cells they are antibodies.

 
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DNA-based logic gates operate inside cockroach cells

DNA-based logic gates operate inside cockroach cells | Complex Insight  - Understanding our world | Scoop.it
The logic units are driven by molecular collisions, not voltage.
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Internet of Things Gains Real World Traction - Automation World

Internet of Things Gains Real World Traction - Automation World | Complex Insight  - Understanding our world | Scoop.it
E&T magazine Internet of Things Gains Real World Traction Automation World More than many other such pronouncements, this statement, made by Jim Robinson of Intel's Internet of Things Group, during a panel discussion at National Instruments' NI...
ComplexInsight's insight:

While IoT is going  through its peak on the hype cycle - stories such as this from Airbus regarding instrumenting the entire production process highlight many of the possibilities. As with any long term technology change, IoT is better described and extrapolated from  the small deploymnent stories that indicate its real future. as opposed to the analyst and booster hype. 

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Are fish far more intelligent than we realize?

Are fish far more intelligent than we realize? | Complex Insight  - Understanding our world | Scoop.it
They don't have a three-second memory. And one researcher thinks we've been dramatically underestimating their intelligence all along.
ComplexInsight's insight:

Culum Brown's research into fish behaviour is deeply revealing both for the insights into aquatic life and into human prejudice regarding other species capabilities.  Good article on vox.com regarding fish sentience, perception and behavioural evolution - worth reading.

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Artificial Life 14

Artificial Life 14 | Complex Insight  - Understanding our world | Scoop.it

ALIFE 14, the Fourteenth International Conference on the Synthesis and Simulation of Living Systems, presents the current state of the art of Artificial Life—the highly interdisciplinary research area on artificially constructed living systems, including mathematical, computational, robotic, and biochemical ones. The understanding and application of such generalized forms of life, or “life as it could be,” have been producing significant contributions to various fields of science and engineering.
This volume contains papers that were accepted through rigorous peer reviews for presentations at the ALIFE 14 conference. The topics covered in this volume include: Evolutionary Dynamics; Artificial Evolutionary Ecosystems; Robot and Agent Behavior; Soft Robotics and Morphologies; Collective Robotics; Collective Behaviors; Social Dynamics and Evolution; Boolean Networks, Neural Networks and Machine Learning; Artificial Chemistries, Cellular Automata and Self-Organizing Systems; In-Vitro and In-Vivo Systems; Evolutionary Art, Philosophy and Entertainment; and Methodologies.

 

Artificial Life 14

Proceedings of the Fourteenth International Conference on the Synthesis and Simulation of Living Systems

Edited by Hiroki Sayama, John Rieffel, Sebastian Risi, René Doursat and Hod Lipson

http://mitpress.mit.edu/books/artificial-life-14


Via Complexity Digest
ComplexInsight's insight:

I remember reading the first one of these and my imagination being captured by Chris Langton's introduction. Look forward to reading this one.

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Gigantic Ocean Vortices Seen From Space Could Change Climate Models | Science | WIRED

Gigantic Ocean Vortices Seen From Space Could Change Climate Models | Science | WIRED | Complex Insight  - Understanding our world | Scoop.it
Enormous vortices of water, measuring 60 miles across, spin their way across the sea at a deliberate pace---3 miles per day.
ComplexInsight's insight:

The role of the oceans is often misrepresented in climate discussions. The discovery of large scale migrating eddies and their potential impact on transportation of nutriends, dissolved carbon dioxide and heat may change our understanding of ocean health and weather. Awesome science article on Wired Science explaining how the phenomenon was discovered and some of the questions it raises - worth reading.

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Quantitative Temporal Viromics: An Approach to Investigate Host-Pathogen Interaction: Cell

Quantitative Temporal Viromics: An Approach to Investigate Host-Pathogen Interaction: Cell | Complex Insight  - Understanding our world | Scoop.it

A systematic quantitative analysis of temporal changes in host and viral proteins throughout the course of a productive infection could provide dynamic insights into virus-host interaction. We developed a proteomic technique called “quantitative temporal viromics” (QTV), which employs multiplexed tandem-mass-tag-based mass spectrometry. Human cytomegalovirus (HCMV) is not only an important pathogen but a paradigm of viral immune evasion. QTV detailed how HCMV orchestrates the expression of >8,000 cellular proteins, including 1,200 cell-surface proteins to manipulate signaling pathways and counterintrinsic, innate, and adaptive immune defenses. QTV predicted natural killer and T cell ligands, as well as 29 viral proteins present at the cell surface, potential therapeutic targets. Temporal profiles of >80% of HCMV canonical genes and 14 noncanonical HCMV open reading frames were defined. QTV is a powerful method that can yield important insights into viral infection and is applicable to any virus with a robust in vitro model.


Via burkesquires
ComplexInsight's insight:

Understanding protein change during virus-host interaction offers opportunities for new diagnostics, treatments and clear understanding of how specific viruses interact and manipulate signalling pathways and immune defenses. QTV offers a lot of promise for researchers and practitioners.

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Machined Learnings: Stranger in a Strange Land

ComplexInsight's insight:

Good article on the differences between big data processing and HPC simulations. Worth reading to see where the two communities focus, worry about and can learn from one another.

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Imagining the Post-Antibiotics Future — Editor’s Picks — Medium

Imagining the Post-Antibiotics Future — Editor’s Picks — Medium | Complex Insight  - Understanding our world | Scoop.it
A few years ago, I started looking online to fill in chapters of my family history that no one had ever spoken of.
ComplexInsight's insight:

Maryn McKenna has consistenly written about the threat of increasing antibiotic resistance for some time and her articles in Wired and other media are worth finding and reading. This is her long form essay on medium, it covers some of the same ground as her other articles it is still very much but its worth reading and reflecting on. 

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Eli Levine's curator insight, April 30, 2014 8:41 PM

It seems that we are about to get closer to death, as our antibiotics, pesticides, herbicides and all other methods of cheating death, disease and crop failure fail.

 

This is before we get into conversations about the looming international and intranational conflicts that are simmering beneath the surface.  At least these can be dealt with with sensible policy changes and changes in attitude, perspective and disposition, if not out right content in our leadership cadres.

 

But alas, I don't see that happening in the foreseeable future.

 

Time is ticking away.

 

And we too will go through an indiscriminate die off phase where friends and family will die off, along with enemies and pestilential people as well.

 

I'd like to think that we'd come off better than before.

 

But, that's the thing about these indiscriminate methods of killing large swaths of the population.  It very rarely yields anything other than what was already present.

 

At least wages should be better, due to the new shortage of laborers (assuming that robots haven't taken over our labor force in the meantime).

 

I'd like to think that our lot is constantly improving, even during these negative phases.

 

But, I know that it's not going to be easy, especially for most of our Western and American population who don't have experience handling these kinds of things.

 

Ah well.

 

Think about it.

 

 

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What Comes After Antibiotics? 5 Alternatives to Stop Superbugs

What Comes After Antibiotics? 5 Alternatives to Stop Superbugs | Complex Insight  - Understanding our world | Scoop.it
"Superbug" bacterial infections that are resistant to common antibiotics are increasing at an alarming rate. But traditional antibiotics aren't the only way to battle dangerous germs. Biomedical scientists are investigating new additions to their arsenal.
ComplexInsight's insight:

Given the WHO announcement that antibacterial resistance is now a global threat - article on popular mechanic outlines some of the alternate treatments to antibiotics.

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bioinformatics-databases

bioinformatics-databases | Complex Insight  - Understanding our world | Scoop.it
Bioinformatics - Databases
ComplexInsight's insight:

Dr.Stefan Gruenwalds scoop-it list of bioinformatics databases is an essential resource for anyone looking to discover which datasets are available and accessible. Awesome.

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Polar Swarms

Polar Swarms | Complex Insight  - Understanding our world | Scoop.it
A new theory can explain the formation of swarming patterns observed in ensembles of self-propelled polar particles.

Via Eugene Ch'ng
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Eugene Ch'ng's curator insight, April 13, 2014 8:27 AM

How do individual animals form swarms, schools, and flocks? In the 1990s, physicists modeled collections of self-propelled particles (so-called “active matter”) and could simulate the ordering that occurs in animal flocks.  Theoretical models have reproduced many aspects of this collective behavior, but a number of questions have persisted. One concerns the observation that in polar, active matter—think of a collection of small, mutually interacting swimming arrows—the particles organize themselves into three possible pattern classes: density waves, solitary waves (solitons), and traveling “droplets.”

No single theory has been able to explain the formation and diversity of these patterns. However, in a paper in Physical Review Letters, Jean-Baptiste Caussin and collaborators from institutes in France, Germany, and the Netherlands, have solved a hydrodynamic model of polar active particles and have accounted for the origin and variety of these propagating swarm structures...

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The Surprising Gut Microbes of African Hunter-Gatherers | Science | WIRED

The Surprising Gut Microbes of African Hunter-Gatherers | Science | WIRED | Complex Insight  - Understanding our world | Scoop.it
In Western Tanzania tribes of wandering foragers called Hadza eat a diet of roots, berries, and game. According to a new study, their guts are home to a microbial community unlike anything that's been seen before in a modern human population -- providing, perhaps, a snapshot of what the human gut microbiome looked like before our ancestors figured out how to farm about 12,000 years ago.
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The race to contain West Africa's Ebola outbreak (Wired UK)

The race to contain West Africa's Ebola outbreak (Wired UK) | Complex Insight  - Understanding our world | Scoop.it
Digital volunteers are racing to map regions in West Africa where the Ebola virus, which has a 90 percent fatality rate, continues to spread
ComplexInsight's insight:

The use of OpenStreetMap (OSM) as an unifying geodata system is increasing in humanitarian aid. The current Ebola outbreak in West Africa is a challenge at multiple levels for teams trying to coordinate a response. Due to years of war there are few up to date maps in the region and multiple boundaries mean different groups are collecting data. Digital volunteers creating new OSM entries will be a key asset in enabling health officials to manage the outbreak and hopefully bring things under control.

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