[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.

[nano technology]

I was reading an article on the super conductor/layered oxide NaxCoO2 that, through various "conducting probe-mediated reversible electrochemical sodium intercalation/deintercalation reactions" information can be written and then erased (I'm sure I'm over-simplifying). In awe of the words used (oxidated, intercalated, superconductivity, nitrogen flux, nanolithographic) and wondering what this might mean for us, the end users of technology led me - via a google search - to a whole new world. A world of a thinking so different from my current, humanities-based research. (it's invigorating to be reminded how we can (or is it just me) get very focused one something which is just a tiny part of a bigger everything) In this world where one can measure conductivity (among a myrid of other things so different from my current examination of multi-mimesis and transliteracy in women-authored web fictions), language and story and critique have the privilege of ephemerality, rather this seems to be a world where experiments are necessary and quantifiable results are produced. One such product is the 3D Atomic Holographic Optical Data Storage Nanotechnology. It is a rewritable holographic removable disk.

"An Atomic / Photonic / Molecular / Quantum / Spintronic / Holographic Switch is the method of using a UV laser atom nanoparticle optical switch defined by a non-contact terahertz nano/microwave electric field modulator using attosecond, femtosecond, terahertz UV photons (electromagnetic radiation) simultaneously to alter properties of ferroelectric molecules for data and light expression. Through the use of UV photon induced electric field poling and dynamically changing the internal geometry of individual ferroelectric atoms in a 3 dimensional optical crystal coated on a high / low velocity substrate.
The UV laser diodes and electric field transducers of the Integrated Read/Write Head can be used in any combination or sequence to control the molecules which include UV/blue photon frequencies and quantum energy level as well as Nano/Micro electro static field strength (voltage) and switching field densities (frequency).The only rub is the cost per bit will be cheaper, faster to access, and faster to store for a much longer time uneffected by many environmental conditons." (see here for more)