Capturing Complexity through Agent-Based Modeling

Another useful and interesting PNAS-supported colloquium.

Signal processing in single cells

Science overview article pointing to two current papers on signal transmission through gene cascades in noisy cellular environments. the article concludes that this work "represents an important advance toward a more quantitative synthetic biology. These studies offer insights into gene regulation, and, together, provide a framework for the further characterization of input/output relationships among regulators and their targets. These quantitative approaches can be applied to natural gene networks and used to generate a more comprehensive understanding of cellular regulation. This will enable a better characterization of individual genetic components and modules, opening up the possibility of designing more complex synthetic gene networks. Such networks could be engineered with specific properties that filter unwanted noise from signaling networks or exploit noise-induced switching to sample more diverse phenotypes."

Bacterial spatial organisation using electrical currents

Nature news article on top down spatial manipulation of bacteria (moving them around a silicon chip) using electrical currents.

Away next week

I'm away all of next week at the Annual Conference on Modelling and Simulation of Biological Processes in the Context of Genomics, Montpellier, France (April 4-8). I'll try to post summaries of talks of interest while I'm there.

Canon move into biotech

Japanese camera and office equipment manufacturer Canon have announced that they are stepping up their interest in biotechnology. Inkjet technology has already been used to spray living cells in very precise patterns, so perhaps some bio-nanotech applications may eventually arise...

Old but good

Collection of papers from a 2002 PNAS Colloquium on Self-organized complexity in the physical, biological, and social sciences.

Away at BCTCS

I'll be giving an invited talk at the British Colloquium for Theoretical Computer Science (BCTCS) in Nottingham, and will therefore be away until Thursday.

Interview with Gordon Moore

Short interview with Gordon Moore (he of "Moores Law", the extrapolated observation that the power of computers doubles every 18 months). He is sceptical about the use of alternatives to silicon as computational substrates, pointing out that mass production of nanotube transistors may prove to be difficult. Of course, the first transistor was a massive, cobbled-together beast of a thing, so I'm not sure of the utility of such observations.

Aliens in the Bible

I appear to have the distinction of being cited in a book titled "Aliens in the Bible". This is fantastic news. My Ph.D. thesis is noted in the references section, sandwiched in between two works titled "The Face on Mars" and "Giant Skeletons". I would draw your specific attention to the section dealing with "artificial intelligence in the Bible". The conclusions drawn are, of course, nonsense - I particularly like the implication in Section 1.6 that my work on "genetically created brains" (sic) may be thought of as an incremental step towards governmental imposition of The Mark of the Beast. Great. First barcodes, now this.

Martyn "668, Neighbour of the Beast" Amos

Nano Wire Cutters

Press release on work done at Purdue University (with reference to forthcoming article) on coating DNA molecules with magnetic nanoparticles. The interesting thing about this work is that the researchers have embedded various restriction sites into the substrate DNA, which allows them to "snip" DNA wires of varying lengths. Presumably, if sticky-ended restriction enzymes are used, with correct strand design (and perhaps use of tiles, such as those developed by Ned Seeman) one could facilitate self-assembly of these wires into larger structures (nano-chainmail, anyone? ;)

Network Dynamics and Congestion

Taster article from the New Scientist (with a link to the full article) on centralisation versus decentralisation, with specific reference to traffic congestion.
The findings may shed light on how and why certain natural systems (such as cellular transport networks) have evolved to be (de)centralised in structure.

Open Source Biology

BIOS, the Biological Innovation for Open Society is an open source biotechnology initiative based in Australia. Along with its parent organization CAMBIA, it aims to foster a "protected commons" for scientific information and technology. Tools and techniques are shared, and can be improved and repackaged, just like in open source software.

Floating Point Errors and Computational Models

A potentially useful and instructive article on the perils of using floating point numerical representations in multi-agent systems.

Followup: Lifewave Energy Patch

No, I'm not being sued, but there is a discussion of the "technology" of the Lifewave Patch on Yahoo! Groups.

Inferring Network Mechanisms: Protein Interactions in Fruitflies

Interesting article in PNAS, looking at the classification of protein interaction networks in fruitflies.

Open Access to Research

Stevan Harnad at the University of Southampton is one of the champions of the open access movement; the idea that full and free access to (often) publically-funded research should be available to all. The momentum behind this concept is growing, and Harnad has been meeting with representatives of the publishing industry in order to thrash out a mutually agreeable strategy. I wish him the best of luck in this endeavour.