Monday, January 29, 2007

Another radio interview

Just a quick note that I'm this week's guest on This Week In Science, a radio show run out of the University of California Davis, and which boasts listeners in over 60 countries. You can either listen online tomorrow at 17:30 (UK) via the website, or download the show later as a podcast.

Wednesday, January 17, 2007

New stuff

Two new publications to report, both very different.

The first is a paper that's just been accepted by BioSystems, and is now available online. Two hybrid compaction algorithms for the layout optimisation problem was written with two colleagues in China, and deals with the problem of packing circular objects inside an "outer" containing circle. Many people will be familiar with this problem, which tries to minimise the size of the container, but our version is complicated by the fact that each object also has mass, and we must seek to minimise not only the radius of the container, but the net mass imbalance. This problem has real-world significance in areas such as aerospace and satellite design, where the circles represent pieces of equipment, and the body as a whole is rotating or moving. We have developed two algorithms, both inspired by nature, which produce the best known results for this problem.

The other piece of writing this month is my first (and quite possibly last) appearance in a men's style magazine (Esquire). As part of their "Hot List 2007", I was asked to write a short piece on "The New Software is...", and chose "Wetware". I'm on page 92 of the February issue, sharing space with George Monbiot.

Monday, January 15, 2007

The next generation

I spent the end of last week and the start of the weekend drifting in and out of the Systems Biology, Bioinformatics and Synthetic Biology conference BioSysBio, which was hosted by the University of Manchester. The event is aimed at post-graduates, post-docs and "young faculty" (I wasn't sure if I qualified for this last descriptor, but they took my money!), and there was certainly a youthful exuberance about the the proceedings. Teaching and family commitments meant that I wasn't able to attend as many sessions as I would have liked, although I was able to make both sessions dedicated to synthetic biology.

The first of these was opened by Randy Rettberg, director of the International Genetically Engineered Machines (iGem) programme. Rettberg had a long and distinguished career as a computer engineer (including serving as the chief technical officer of Sun Microsystems) before turning his attention to biology and dividing his time between iGEM and looking after MIT's Registry of Standard Biological Parts, the community's attempt to do for synthetic biology what the Maplin Catalogue did for electronics.

There then followed three talks by UK-based teams who took part in the most recent iGEM. The Imperial College team described their novel approach to building a cell-based oscillator (a device that gives a signal that goes "up" and "down" on a regular basis). Rather than building their oscillator inside a single cell, as others have done, the Imperial team decided to try to model classical "predator-prey" dynamics, where the population of prey (eg. rabbits) rises and falls slightly out of step with the rise and fall in the number of predators (eg. foxes). The students decided to engineer two populations of bacteria, each generating molecules that would cause the net signal between the two to rise and fall periodically. Although they've yet to get it all working together, it's a novel approach to the problem, and their simulations and early experimental characterisations seem to suggest that they're well on the road to success.

Another talk was given by a team from Cambridge, who were investigating a subject close to my own heart; self-organisation and pattern formation in bacteria. They've harnessed the ability of bacteria to "swim" combined with an engineered position-dependent genetic "switch" to generate spatial patterns from the "bottom up". The ability to be able to control this process may have significant implications on tissue engineering and bio-medicine, as we'll see shortly.

For me, the most inspiring student presentation was given by the group from Edinburgh, about whom I've written briefly in my book. Arsenic contamination in drinking water is a problem that affects tens of millions worldwide, and is particularly acute in Bangladesh. Existing methods for testing samples are expensive and require technical training, so the Edinburgh team have developed a cell-based detection kit that can detect concentrations below the WHO safety threshold, and which produces a simple "yes-no" response that a non-specialist can understand. Their eventual objective is to be in a position to package and sell the kits for around $1 a pop, which will make sustained testing possible for villagers. A fantastic technical achievement as well as an extremely worthy cause.

I felt slightly humbled by the experience of watching these students in action; remember, most of them were undergraduates (albeit the best of the best) when this work was carried out, and yet they were doing work that, only a few years ago, would be considered the absolute state of the art, and attracting Science and Nature papers (although I can't see any reason why the current work should not do the same). If any of them choose to pursue a career in this field (and I sincerely hope that they do) then they have an excellent future ahead of them.

The final plenary was given by my colleague Ron Weiss of Princeton, who is one of the leading figures in synthetic biology (and, again, who features prominently in the final chapter of my book). Ron has been at the forefront of cellular re-engineering for some years now, and has consistently produced first-rate work. Ron is also interested in pattern formation in nature, and his recent work focuses on programming the way that stem cells talk to other cells, in the hope of one day being able to control the way that they "specialise" and form tissue structures. Although it's still very early days, I think this work has the potential to be massively significant.

Monday, January 08, 2007

A good way to start the year

A (belated) Happy New Year to you!

I haven't, up until now, flagged reviews of Genesis Machines on the blog (partly because I assume that most people who come to it have arrived via the link in the book). However, I was delighted by this review in last Saturday's Guardian; apart from saying nice things about the book, its author, Steven Poole (who wrote Unspeak) appears to share my views on Melanie Phillips of the Daily Mail.

A minor point: Poole ends his review by saying that "It is even possible that, when the footnote numbering goes crazy on pages 199-201, it is some sort of joke about genetic mutation. Sadly, I was not able to find meaning in the resulting number series." He assumes that footnote numbers refer only to the first citation of a source; in the example he gives, I cited a report at the start of the chapter, and then again near the end. In both instances I supplied the reference number ("3"), which is why it might have appeared to be out of sequence later on.