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
Enormous vortices of water, measuring 60 miles across, spin their way across the sea at a deliberate pace---3 miles per day.
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.
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.
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.
A few years ago, I started looking online to fill in chapters of my family history that no one had ever spoken of.
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.
"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.
Given the WHO announcement that antibacterial resistance is now a global threat - article on popular mechanic outlines some of the alternate treatments to antibiotics.
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.
Digital volunteers are racing to map regions in West Africa where the Ebola virus, which has a 90 percent fatality rate, continues to spread
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.
Many varieties of fruit, meat and vegetable are disappearing from our plates, says Rachel Nuwer. Why is this happening, and can we stop the rot?
Its probably not often we stop to think of the impacts of agriculture on the evolution of foodstuffs and what varieties of plants are being lost, along with their distinct tastes, benefits and properties. Compared to pre 1900 agriculture an estimated 75% of global farmed plant diversity is now gone and lost. Diversity is key to sustainable agriculture over the long term, so the points made in the article are particularly worrying. Thought provoking article from the BBC / worth reading.
Use Google Flu Trends as an example of how things go wrong.
Good article on risks of interpreting large scale data mining using google flu trends as an example. The conclusion that often data indications are a first point of a process that then requires scientific grunt work to identify if a given correlation is actually relevant or not and that reality is sometimes the grunt work wont be done because its hard, requires funding and takes time. Worth reading.
Three Impediments to the Internet of Things - blog post by Walter Dick of Ascent Venture Partners
Walter Dick believes the major impediments for IoT are:
1. Networks are not up to Par..
2. Security needs to improve
3. Batteries need innovating
Not sure I agree 100% on his top 3 but they are certainly contributing factors. Companies like Blackberry and Nokia Oyj (the parent company of the phone manufacturer recently purchased by Microsoft) are incredibly well placed to deliver IoT in terms of network and security and have expertise for power management. Unfortunately Blackberry is not focused on IoT much at all and is beset with its own problems. I am more hopeful on Nokia Oyj / now they have hived off the phone business they retained the networking infrastructure and mapping divisions along with the expertise in power electronics. It would be interesting to see them pioneer in the IoT area as they once did with mobile phones...
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.
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.
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.
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.
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.
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.
New WHO report provides the most comprehensive picture of antibiotic resistance to date, with data from 114 countries
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.
Evidence from Southwestern deserts suggests that oxygen-breathing organisms arose on land rather than in the seas.
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.
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.
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.
When it comes to our immune response, genetics takes a back seat to pathogens.
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.
Evidence from skulls in east London shows plague had to have been airborne to spread so quickly
With the exhumation of 25 skeletons, originally buried in the mid 14th Century scientists in London are discovering new clues which indicate the black death was an pulmonary airborne disease. Good article in the Guardian on the initial findings.
Jorge Titinger, CEO of SGI has a good article on applications of HPC to Big Data including:
Graphing and mapping: HPC-powered data mapping and graphing will lead to greater accuracy in business forecastingPattern visualizations: HPC-powered tools will emerge that can provide an intuitive view of complex data sets, enabling rapid identification of relationships for simple analysisScaling in-memory databases: HPC will allow enterprise in-memory systems to handle larger data workloads — allowing closer to complete data sets (over partial sets) to benefit from real-time analytics while in motionMeta-data: The importance of meta-data will jump dramatically — we’ll see enterprises realize leveraging meta-data analytics for virtualization and relational mapping can yield enhanced accuracy, new business insights and even reveal security threats
With the advent of on demand compute and cloud based processing it will be interesting to see how the HPC companies continue to differentiate from on demand suppliers such as amazon and microsoft. Jorge's 2014 outlook is interesting and more sane than many big data predictions - certainly worth reading.