Sunday, June 01, 2008

Synthetic biology and Howard Hughes

The Howard Hughes Medical Institute has announced its latest set of investigator appointments. Awards are made to individuals, as opposed to the usual mode of funding, where money is assigned to a project, and the field of synthetic biology is represented by two of its leading figures in the current crop. Jim Collins at Boston and Michael Elowitz at Caltech both had papers in the important 2000 issue of Nature, which reported some of the first experimental results in the area (specific papers are here and here.)

Thursday, May 29, 2008

Genesis Machines in the USA

I'm pleased to report that Genesis Machines has just been published in the USA by The Overlook Press. The book is available via Amazon, and I'm delighted to be associated with another independent award-winning publisher (after Toby Mundy's 2005 triumph with Atlantic at the 2005 British Book Awards).

Sunday, February 24, 2008

Engineering biology, with Drew Endy

There's a fascinating essay by/interview with Drew Endy on the Edge website, which appears to be the latest in a series to have emerged from an event they organised last August. I've written about Endy in the past, and he features prominently in the final chapters of Genesis Machines; indeed, I wish I'd had such an illuminating transcript available when I wrote the book.

Endy is an Assistant Professor of Biological Engineering at MIT, and one of the leading figures in synthetic biology. In one particular paragraph, he captures the excitement of this emerging new discipline:

"Programming DNA is more cool, it's more appealing, it's more powerful than silicon. You have an actual living, reproducing machine; it's nanotechnology that works. It's not some Drexlarian (Eric Drexler) fantasy. And we get to program it. And it's actually a pretty cheap technology. You don't need a FAB Lab like you need for silicon wafers. You grow some stuff up in sugar water with a little bit of nutrients. My read on the world is that there is tremendous pressure that's just started to be revealed around what heretofore has been extraordinarily limited access to biotechnology."

Friday, February 15, 2008

Insect lab

I've spend all week running simulation experiments for our ongoing work on ant-based computing, so when I came across the Insect Lab it seemed strangely appropriate.

The artist takes real (dead) insects and customizes their bodies with parts taken from watches and other mechanical devices, to create "cybernetic sculptures".

I'd like to see him do an ant, though... Which train of thought lead me circuitously to Bill Bailey performing his wonderful song Insect Nation (if you just want the lyrics, they're here).

Friday, February 08, 2008

Dr Who

A wonderful present arrived in today's post, courtesy of our equally wonderful friend Eventhia; a signed photograph of Tom Baker! He is, of course, best known for playing the fourth Dr Who, but is probably most familiar to a younger generation as the narrator of Little Britain (and even the delightfully barmy Stagecoach adverts).

Most people of sound mind would name Baker as the best ever Dr Who, despite ludicrous polls to the contrary. A case can be made that the choice of favourite depends on which Doctor a person grew up with, and since Baker's tenure extended from 1974-1981, I would certainly agree.

Anyway, he recently did a signing in Norwich, attended by our friends Kris and Eventhia. They very kindly got Tom to sign the photo "For Martyn," (eventually, I think he had it down as "Martin", and you can see where he's corrected it at E's prompting) "Genetically yours, Tom Baker"


Tuesday, February 05, 2008

Biological complexity: from molecules to systems

I'm delighted to have been invited to speak at an event titled "Biological complexity: from molecules to systems", to be held at University College London from 12-13 June this year. The meeting is sponsored by both UCL and the Weizmann Institute of Science in Israel, and will feature speakers from the fields of immunology, computer science, mathematics, biological chemistry, molecular genetics and bioinformatics. I'll try my best to summarize below the research interests of the other invited speakers (but apologies to anyone whose work I misrepresent!)

Stephen Emmott from Microsoft Research in Cambridge will give the keynote address. Stephen is the founder and Director of Microsoft's European Science Programme, and was the driving force behind the influential Towards 2020 Science project and report.

Representing Israeli activity, Nir Friedman works in computational biology, and recently published a paper arguing that gene duplication may drive the "modularisation" of functional genetic networks (that is, genetic networks that are relatively self-contained, and which perform a specific task).

David Harel is a celebrated computer scientist, having carried out important work in logic, software engineering and computability theory. As a student, I often referred to his award-winning book Algorithmics: The Spirit of Computing, and he is currently working on topics that include the modelling and analysis of biological systems (eg. the nematode worm) and the synthesis and communication of smell.

Shmuel Pietrokovski works in bioinformatics, with particular interest in inteins (protein introns); "selfish" DNA elements that are converted into proteins together with their hosts.

Yitzhak Pilpel's lab takes a systems-level approach to how genes are regulated: "By applying genome wide computational approaches, backed-up by in house laboratory experiments, [the lab] devotes itself to both establishing an in-depth understanding of the different processes controlling gene expression, and to understand[ing] how these processes are orchestrated to establish robustness of the regulatory code."

Gideon Schreiber studies the precise nature of protein-protein interactions and the implications these have for complex biological processes.

Eran Segal is a computer scientist (predominantly) working in computational biology, who has recently reported some fascinating work on a "higher level" genetic code, as well as research on predicting expression patterns from their regulatory sequences in fruit flies.

I've already written at some length about Ehud Shapiro (also here); his recent work has centred on the construction of biological computing devices (known as automata) using DNA molecules and enzymes.

Yoav Soen's group is "using embryonic stem cells models to study how different layers of regulation interact to specify morphogenetic decisions, how these decisions are shaped by interactions between emerging precursors and how they are coordinated across a developing embryonic tissue." He has also worked with a colleague of mine, Netta Cohen at Leeds.

Representing activities in the UK, we have Cyrus Chothia from the Laboratory of Molecular Biology at Cambridge, who studies the "nature of the protein repertoires in different organisms and the molecular mechanisms that have produced these differences."

Jasmin Fisher is leading the new Executable Biology Group at Microsoft Research, and is primarily interested in systems/computational biology.

Mike Hoffman and Ewan Birney are at the European Bioinformatics Institute (EBI) in Cambridge, where Birney leads the EBI contribution to Ensembl. There's a transcript of an interview with him here.

Jaroslav Stark is the Director of the Centre for Integrative Systems Biology at Imperial College. He was recently interviewed for a piece on systems biology on BBC Radio 4's The Material World.

Michael Sternberg heads the Structural Bioinformatics Group and the Imperial College Centre for Bioinformatics. He was previously the head of biomolecular modelling at the Imperial Cancer Research Fund now part of Cancer Research UK.

Perdita Stevens is at Edinburgh, where she works on software engineering and theoretical computer science (with a growing interest in modelling viral infection).

The meeting organisers are particularly keen to encourage the participation of young researchers, and the registration fee for this two-day event is a very reasonable 50 pounds (30 for students). To register and for further information, please contact Michelle Jacobs at Weizmann UK at or on 020 7424 6860. Attendance will be limited to 180 delegates.

Thursday, January 31, 2008

The human genome, in book form

I've just been sorting through some old files, and came across this picture (click for a larger version), which I took on my last visit to London. I had some free time before a meeting at the BT Tower, so I popped into the Wellcome Collection.

Quite apart from the fact that the Wellcome Trust spends around 400 million pounds a year on biomedical research, I have a personal affinity with the trust, since my shortlisted entry to their Book Prize (which was won that year by Chris McManus' Right Hand, Left Hand) was picked up by Toby Mundy and eventually evolved into Genesis Machines (pictured below in the Wellcome Collection bookshop, in a nice circular turn of fate).

One of the most striking exhibits they have (alongside a sample of droppings from Dolly the sheep) is the human genome, printed out in book form. As I've said before, we're rank amateurs compared to nature in the information storage stakes (of course, reading and writing data quickly is another matter...) Since the size of the human genome is estimated at around 3 billion genetic letters (taken from the set {A, G, C, T}), then (assuming that one byte is used to store each letter), each cell with a nucleus (that is, every one except red blood cells and the like) contains 3 Gigabytes of genetic "memory". Of course, we don't need an entire byte (8 bits) to store a quarternary (base 4) value, so we could compress this figure by three quarters, and cells actually contain two genomic copies, but I don't want to over-complicate things...

The fact of the matter is that our genome is large: in the past, I've compared it, if printed out in full, to 200 copies of the Manhattan telephone book. This analogy was arrived at by some back-of-an-envelope calculations, and I don't think I really understood its significance until I visited the Wellcome Collection.

There, in a corner of one of the galleries, stand a single set of white shelves, almost 5 metres by 2 metres, containing 120 hefty volumes. One of them stands open, and a closer inspection reveals page upon page of genetic data, rows and rows of A's, G's, C's and T's tightly-set in 4.5-point text.

The sheer scale of the artifact is mind-blowing, both as an illustration of nature's nanotechnology, but also as a reminder of how far we have to go in terms of beginning to piece together even a small fraction of the human circuitry.

Tuesday, January 29, 2008

Sex with robots

One of the sure signs of impending middle age, especially in a university town, is when people stop handing you flyers. There was a time not so long ago when I could nip out of the office for a sandwich and come back burdened with glossy adverts for progressive house, 2-for-1 vodka shots and foam. But no longer. Now, the bright young things actively avoid me as my thirty-something, corduroy-clad figure shambles into view. The kinder ones simply pretend not to see me.

So imagine my delight when, walking down Oxford Road this afternoon after picking up some grapes, I was handed a flyer. And one offering sex with robots, to boot! Impressed by the targeted precision of whoever was marketing such an opportunity, I was about to kick my heels when I realised that it was actually advertising a club night in Manchester. Now, as a long-time veteran of nights such as House of God and Voodoo, I might have been interested...ooh, ten years ago, but with a responsible job and a young daughter, "'avin it large" now means having that third shot of espresso in my cappucino.

Which is a really cheap and tenuous way of introducing a new play that I think you should go and see. Involution is by a new author, Rachel Welch, and deals with many urgent contemporary themes, such as genetic engineering, religion and the human self-image. One of the plot threads concerns "cybernetic companionship", so I'll leave it to you to make the link...

Alfie Talman, a member of the production team and cast (and, coincidentally, a fellow Ipswich fan) enjoyed Genesis Machines, and thought I might be interested in the play. It's on from February 21st to March 15th at the Pacific Playhouse in London, and there are more details here (and here).

Monday, January 14, 2008

"I'm burning, I'm burning!..."

Although every side in an argument tends to have its own complement of fools, the idiocy exhibited by fundamentalist Christians, in debates over evolution or the origin of the universe, often takes us into the realm of comedy.

Take this example, lifted from a list of fundie "bloopers":

"Everyone knows scientists insist on using complex terminology to make it harder for True Christians to refute their claims.

Deoxyribonucleic Acid, for example... sounds impressive, right? But have you ever seen what happens if you put something in acid? It dissolves! If we had all this acid in our cells, we'd all dissolve! So much for the Theory of Evolution, Check MATE!"

The full amusing-and-yet-slightly-scary list is here.

Tuesday, January 08, 2008

Genesis Machines in Japan

Readers in Japan may be interested in the forthcoming edition of Genesis Machines, which is now available for preorder. It's been translated by Kyoko Gibbons, and is out on the 17th of this month.