[bacteria rule: organic computing]

Some interesting developments in organic computing noted in a recent article from the Journal of Biological Engineering:

Background

The Hamiltonian Path Problem asks whether there is a route in a directed graph from a beginning node to an ending node, visiting each node exactly once. The Hamiltonian Path Problem is NP complete, achieving surprising computational complexity with modest increases in size. This challenge has inspired researchers to broaden the definition of a computer. DNA computers have been developed that solve NP complete problems. Bacterial computers can be programmed by constructing genetic circuits to execute an algorithm that is responsive to the environment and whose result can be observed. Each bacterium can examine a solution to a mathematical problem and billions of them can explore billions of possible solutions. Bacterial computers can be automated, made responsive to selection, and reproduce themselves so that more processing capacity is applied to problems over time.

Results

We programmed bacteria with a genetic circuit that enables them to evaluate all possible paths in a directed graph in order to find a Hamiltonian path. We encoded a three node directed graph as DNA segments that were autonomously shuffled randomly inside bacteria by a Hin/hixC recombination system we previously adapted from Salmonella typhimurium for use in Escherichia coli. We represented nodes in the graph as linked halves of two different genes encoding red or green fluorescent proteins. Bacterial populations displayed phenotypes that reflected random ordering of edges in the graph. Individual bacterial clones that found a Hamiltonian path reported their success by fluorescing both red and green, resulting in yellow colonies. We used DNA sequencing to verify that the yellow phenotype resulted from genotypes that represented Hamiltonian path solutions, demonstrating that our bacterial computer functioned as expected.

Conclusions

We successfully designed, constructed, and tested a bacterial computer capable of finding a Hamiltonian path in a three node directed graph. This proof-of-concept experiment demonstrates that bacterial computing is a new way to address NP-complete problems using the inherent advantages of genetic systems. The results of our experiments also validate synthetic biology as a valuable approach to biological engineering. We designed and constructed basic parts, devices, and systems using synthetic biology principles of standardization and abstraction.

Another article of interest published in January in New Scientist on organic computing is here.

[rim competes with apple's app store]

Copied from Larry Dignan's article on zdnet:

"Research in Motion launched its BlackBerry application store—dubbed App World—and the pricing model will immediately draw comparison’s to Apple’s App Store set-up. That comparison, however, only goes so far.

For starters, RIM’s App World pricing model has raised a bit of a ruckus since it veers a bit from Apple’s scheme (Techmeme). But a business audience isn’t going to sweat a $2.99 application compared to a 99 cent minimum priced app. And RIM’s audience is likely to even pay higher prices if the App World can actually deliver software with a real business use. And there are so many tiers to the App World model that RIM could have said “charge what you want.”

But the biggest takeaway from the App World pricing model is that higher prices mean more for developers (see FAQ). RIM needs more developers on its bandwagon since the iPhone is the shiny object in the mobile world. Simply put, money talks and RIM plans to use it. Matthew Miller notes that RIM’s pricing model shouldn’t be that big of a deal.

Sure RIM does offer free apps, but developers aren’t likely to offer them. Given developers pay an upfront fee why would you pay RIM to distribute a free app? RIM’s message with App World appears to be: Frivolous and fun apps need not apply.

Will RIM’s App World work?

My hunch is that RIM’s App World will do well, but isn’t going to a success as measured by Apple’s store. RIM’s store is likely to be more BlackBerry-ish—the applications will be more business focused, tool oriented and won’t feature hot games.

RIM also has an app management issue on its hands. Apple’s App Store has to support just the iPhone and iPod touch. RIM’s applications will work on these models:

• BlackBerry Bold 9000 smartphone
• BlackBerry Storm smartphone
• BlackBerry Pearl Flip Series
• BlackBerry Curve 8300 Series
• Black Berry Curve 8900 smartphone
• BlackBerry 8800 Series
• BlackBerry Pearl Series

The experience on all of those models will vary. For instance, a game on the Storm will be different than the Bold and Curve. How will RIM navigate that conundrum? As a developer those models mean more complications.

Other takeaways from the RIM App World effort:

• A PayPal account is required with App World for customers and developers;
• Developers from around the world can contribute except for those from Belarus, Myanmar/Burma, China, Cuba, Iran, North Korea, Sudan and Syria.
• To submit an application there’s a $200 fee, which will be refunded if the software is rejected."

[forecasting the future: newspapers "by" computer]

"The new tele-paper won't be much competition..." (says the news anchor in 1981):

[transdisciplinarity and knowledge cartographies]

As I discuss research projects, aims and future developments with IOCT researchers and affiliates, I'm realising more and more that we're often talking about the same (or at least similar) things though we're using a different language to describe our systems and processes. A recent paper by Josianne Basque, Gilbert Paquette, Beatrice Pudelko and Michel Leonard on "Collaborative Knowledge" suggests the use of a mapping tool as a way of tracing where knowledges crossover and supports the "externalising" of knowledge. Although this tool (MOT) is primarly discussed in terms of sharing knowledge between experts and novices, something like this visual mapping would be useful in the sharing of knowledges between disicplines too.



There are loads more interesting papers in the edited collection Knowledge Cartography: Software Tools and Mapping Techniques including ones that focus on knowledge mapping and curriculum development.

[postdoctoral research fellowships at the ioct]

Two fantastic opportunities to work at the IOCT:

Postdoctoral Research Fellow (two posts)

Institute of Creative Technologies (IOCT)

Three years fixed term

£29,138 - £31, 840 pa

You will work on ‘DMU Creative', a project which aims to provide a commercial showcase for the best creative work in the East Midlands by establishing a quality threshold and an advanced content management system. This project is funded by the HEIF (Higher Education Innovation Fund), which is an HEFCE funding stream designed to encourage and facilitate knowledge transfer, collaboration and outreach, in support of the development of innovative goods, services and policies. The undertaking or possession of a PhD is essential.

The two Research Fellows will work closely together to ensure a co-ordinated project. Responsibilities will include literature research, experimental work, software development, field trials, project documentation, seminar/workshop, technical/academic papers and laboratory support. The work will involve travelling within the UK.

Post 1 (ref. 5062): You will, in the first instance, establish a record label and associated internet radio station to connect with a large number of SMEs and micro-businesses working in music production across the region. This will be followed by similar endeavours in other fields of creative production. You will be based in the Music, Technology and Innovation Research Centre, which is a partner of the IOCT.

Post 2 (ref. 5063): You will undertake the creation of an advanced content management system that utilises broadband to bring the creative resources of the region together, to create a portal which promotes the regional creative works nationally and internationally, to establish by making them commercially available over a variety of connected devices, including TVs. You will be based in the Mechatronics Research Centre, which is also a partner of the IOCT.

Please quote relevant reference number.

Closing date: 7 October 2008.

Application forms and further details are available from our website: www.jobs-dmu.co.uk.

Alternatively telephone 0116 250 6433 (24 hour answerphone).

Or write to:
The Human Resources Team, De Montfort University, The Gateway, Leicester LE1 9BH.