My home page (and this blog)

I've redesigned my home page: I think the design looks cleaner (and more consistent with the blog). I've also added navigation bars at the left, so hopefully it looks a bit more professional. I've also added a photo gallery section to this blog (it's rather sparsely-populated right now, but will become more interesting once I've had a chance to file a load of existing pictures). Comments are, of course, always welcome.

Little green hackers

If you've seen the film Independence Day, you'll know that the Earth was saved by Jeff Goldblum's geeky scientist character inserting a virus into the main computer system of the alien mothership. In addition to Goldblum, we clearly have to thank Microsoft's marketing team, as, remarkably, the aliens appear to be running a variant of Windows on their server (as my colleague Susan Stepney has highlighted), making them vulnerable to attack.

Of course, this is just sci-fi licence, and nobody seriously believes that even Bill Gates has managed to achieve intergalactic penetration. Or has he? Richard Carrigan clearly thinks so, as he's recently raised concerns that the Search for Extraterrestrial Intelligence (SETI) may run the risk of inadvertently introducing alien computer viruses into our global computer network. His forthcoming journal article (subscription might be required) describes his "SETI hacker" hypothesis in rather more detail.

I'm sure Dr. Carrigan is trying to make an important point, but I'm afraid it's somewhat undermined by the implied understanding of how operating systems and viruses actually work. To quote from his article:

At least two scenarios need to be considered in protecting against a malevolent SETI Hacker signal. One is a computer virus in the message that takes over the computer at the receiver. The other is an open message that gives an impenetrable software code or instructions for a hardware translator to handle an opaque message. Both cases are dangerous. The damage may be done before the receiver appreciates that it is under attack. This is the current experience even with Earth-based hacker attacks. There may not be an opportunity to pull the signal out of the computer or turn off the power before the intruding signal has taken over.

Computer viruses can only "take over a computer" if

• They are written in the native machine language of the computer, or are present in some other "executable" form (eg. a macro),
  
• They are then actually executed
  

Even if the signals being decoded by SETI did contain an alien virus, it's extremely unlikely that it would encode executable code that could infect a human-constructed machine. Even if it did, we would still have to then knowingly run it, so I think we can safely rule out alien hacker attack in the near future. However, I have an open mind, and will happily reconsider the possibility of inter-stellar crime if (for example), I receive an email from Councillor Zarg of the planet Cthu-Targ9, asking for my absolute discretion in transferring 3.5 million Galactic Credits from his father's bank account...

This week's Nature

This week's issue of Nature is chock-full of good stuff (a lot of which, unfortunately, requires a subscription). It's a special issue on synthetic biology, an exciting new research area at the intersection of biology, engineering, computer science and mathematics (amongst other disciplines). According to the main website in the field, synthetic biology refers to

• the design and construction of new biological parts, devices, and systems.
  
• the re-design of existing, natural biological systems for useful purposes.
  

Essentially, researchers are trying to work out the "parts catalogue" for living organisms, and then seeing how these components can be put together in new ways to yield entirely new behaviours, as well as investigating how the existing components may be re-engineered to make them more efficient, react to different inputs, etc. According to the editorial, "This technology allows biological components, circuits and potentially replicating organisms to be developed from scratch, possibly based on different genetic codes from those found in the wild."

A lovely example of synthetic biology in action is the bacterial "camera", which uses engineered E. coli bugs (there's an open access Science Daily press release). Some of the founders of this new field describe recent progress, discuss its foundations, and consider the ethical and safety issues that such research must address.

In an unusual step for the journal, they've also commissioned a cartoon guide to synthetic biology (which is open access).

I'm currently writing a journal article on "Bacterial Self-Organisation and Computation", which will describe a lot of this work - I'll post a link to it when it's finished.

Dreamlines

Dreamlines is a beautiful image generation website that takes a search query, passes it to Google Images and then processes relevant pictures to draw a "dream-like" progression. The interesting thing, from my perspective, is how the images are processed - a graphic file provides the template "environment" for a group of interacting particles, or agents, which interact in a non-linear fashion to generate an emergent whole (more on this paradigm here).

I'm not sure about the waffle about the internet "dreaming", but it does generate a lovely series of images (I tried DNA and bacteria, both with nice results).

The site does require Flash and Java.

Online biology books

This is a wonderful resource for anyone working in the life sciences (or at an interface thereof). The National Center for Biotechnology
Information (NCBI) is responsible for collecting, organising, facilitating access to and disseminating knowledge about molecular biology, biochemistry and genetics.

The Bookshelf is a fully-searchable collection of biomedical texts (including some classics).

The Ants and the Airbus

I was very lucky in the last academic year to work with two very bright students on a couple of agent-based computing research projects. One of these was Oliver Don, and our work on modelling ant colonies is reported below.

The other student was Andrew Wood, and we decided to investigate the evacuation of the new Airbus A380 (the first ever double-decker passenger aircraft). Where this aircraft differs from those that have gone before is that the upper-deck exits are significantly higher than those on standard aircraft, and we wondered if "door delay" (ie. hesitation induced by the realisation of just how high the exit is) would have a significant impact on the time taken to evacuate the aircraft. In order to investigate this, we built an individual-based model of the aircraft (basically, model each individual passenger, each with their own particular attributes, and then "let it run"), and I think we came up with some interesting findings. The most significant conclusion we drew was that if average door delay exceeds just over 1s, then the aircraft will fail its certification trial (which requires it to be fully evacuated of passengers and crew within 90s).

Of course, this is just a prediction based on a simplistic model of the aircraft, but previous small-scale studies with real people have suggested that door delay will play a significant role. We await with interest the results of the full certification trial (which has yet to take place).

An article based on this work is currently in submission to a journal, but the project web page points to a pre-print version of it. There's also a version of the simulation that you can run in your browser and play with. In the mean time, I'll post an update when I hear anything about the progress of the paper, but this post is also meant to flag a forthcoming documentary, which I believe is showing in the UK this Friday (25th November) on Discovery Wings.