24 I N T E R N A T I O N A L P A G E
UK 7 - 9 OKTOBER 2008
Biology’s LEGO bricks
What the
bleep
is...?
| R E P O R T | Synthetic biology is a new science that aims to create purpose-built organisms. The building blocks are bits of DNA. A group of students from the University of Groningen is building a cellular automaton in this fashion. It’s their entry for an international Synthetic Biology competition.
Fortis
By ERNST ARBOUW “It’s quite hard to give a good definition of synthetic biology”, says student Auke van Heel. “Everyone working in the field seems to have his own interpretation of what it actually is.” Van Heel and fellow biology student Martijn Herber are part of a team of nine students from the University of Groningen who are competing in IGEM, an international synthetic biology design competition for students, organized by the renowned Massachusetts Institute of Technology (MIT). In four weeks time they’ll travel to Boston to present the project they have been working on for the last ten months: a cellular automaton made from bacteria. “Imagine you have a large box of LEGO bricks that can be combined to build all kinds of objects. That’s more or less what synthetic biologists do”, explains Van Heel. The ‘LEGO bricks’ are in fact genes, each with their own distinct, welldefined properties. By combining the bricks within a micro-organism like a bacterium, it is possible to make something completely new, an organism with a number of specifically designed capabilities. The main difference between synthetic biology and more traditional microbiology is that synthetic biology starts with nothing more than a set of building blocks – genes that come from organisms as diverse as deep-sea fish and ancient bacteria – and a vision of what to build with them. “Traditional microbiology research starts, generally speaking, with an existing organism, like a bacterium or a fungus, and then studies how to change certain aspects of its behaviour. We began with a picture of what we wanted to build and then started combining the bricks that were necessary to build it.” The students started their project in early 2008 with a number of brainstorming sessions and joint tutorials. Because they had different academic backgrounds – they were not only biology students but also physics, chemistry and com-
Biologists unravel penicillin genome A team of biologists working at the University of Groningen, Delft University of Technology and the multinational DSM have analysed the entire DNA sequence of Penicillium chrysogenum, the fungus that produces the antibiotic penicillin. Their results were published in the scientific journal Nature Biotechnology last week. The genome sequence of the Penicillium fungus may help to refine the organism at a molecular level and thereby increase penicillin production, says Gro-
Martijn Herber (left) and Auke van Heel puter science students – there was a lot of brushing up to be done. “That was very instructive”, says Herber. “Not only on a practical level; it also showed that different scientific disciplines each have their own, slightly different way of approaching and tackling problems.” “It was interesting to see how physicists tend to take a very functional approach: I want the organism to do A, so I must use building block B to produce protein C. Biologists tend to take a more fuzzy approach: to get from A to C, B might actually work.” “Compare it to a pointillist paint-
ing”, adds Herber. “When you push your nose against the canvas you see individual dots, each with their own colour. They are the individual building blocks. When you take a few steps back you see the colours blend and form pictures.” The team eventually settled on three possible ideas: creating a biological pump, creating memory DNA to store information in microbial cells, or making a cellular automaton, a grid of cells that evolves according to a limited set of fi xed rules [See: What is a cellular automaton]. They decided on the third project.
What is a cellular automaton? A cellular automaton is a collection of cells on a grid which evolve through a number of stages according to rules based on the states of their neighbouring cells. These rules are then repeatedly applied. A simple example would be a row of ten randomly chosen numbers that evolve via a simple rule: odd numbers are multiplied by three, even numbers are multiplied by two. After each step, the ten new numbers are printed above the previous line to form a table. By adding a few simple rules – for example, subtract the number on the left-hand side before multiplying, unless it is a prime number – it is possible to allow the table to develop in a seemingly unpredictable way. Cellular automata were first developed by the Polish mathematician Stanislaw Ulam in the 1940s while he was working on the development of the first nuclear bomb in the Los Alamos Laboratory.
Photo Jeroen van Kooten Herber shows a portfolio with the IGEM competition logo. In it are pieces of heavyweight paper with yellow dots that are a little under a centimetre in diameter. “This is our standard IGEM LEGO toolbox”, he says. The yellow dots contain small fragments of DNA. “Once you decide to use a certain building block, you can punch out the corresponding yellow dot and use it in a micro-organism”, Van Heel says. And then the real work starts: every time a building block is added it must be tested to see if it works and to see if it actually does what it should do. So do they now have a fully functioning bacterial cellular automaton, designed and built in the lab? Not exactly. “Yesterday was a very bad day for science”, they laugh. “We did a test to see if our construction did what it was supposed to do, but sadly it didn’t”, says Herber. But, he adds, that doesn’t mean the team’s trip to Boston will be cancelled. There is even a chance that the students will still win a prize in the competition. “A fully functioning micro-organism is not the main requirement of the competition. “We’re still going to the conference to present our research and to show what we tried to achieve.” “And to have a good time”, Van Heel quickly adds.
Last Friday evening the Dutch government announced that it had nationalized parts of the DutchBelgian bank and insurance company Fortis. The nationalization followed last week’s bail-out plan in which the Dutch, Belgian and Luxembourg governments acquired 49 percent of the shares in the company. Despite the investment of EUR 11.2 billion by the three governments, the bail-out proved insufficient to solve the bank’s financial problems. Shortly after the first rescue plan was announced, the Dutch and Belgian governments commenced secret negotiations that would eventually lead to the nationalization of the company’s Dutch assets. The deal involves an investment of EUR 16.8 billion by the Dutch government. Fortis ran into trouble after taking over ABN Amro, one of the largest banks in the Netherlands, shortly before the credit crunch. Finance minister Wouter Bos told journalists that the nationalization of the bank was necessary to prevent its bankruptcy. He said the deal was essential for the stability of the Dutch banking sector. Bos also said that the nationalization of the bank was a temporary move. Fortis will be sold as soon as the financial crisis subsides. [ ERNST ARBOUW ]
Afghanistan ningen molecular biologist Prof. Arnold Driessen, one of the authors of the Nature article. The researchers discovered that its DNA contains 49 ‘sleeping’ gene clusters, which may enable the fungus to produce substances that may also serve as antibiotics. “Penicillin may just be the tip of the iceberg; this fungus may be capable of much more than we know now”, says Driessen.
Students with toy weapons arrested Nine students from Delft University were arrested in Dordrecht,
near Rotterdam, last Friday for breaking the Arms and Munitions Act. The students were on their way to Belgium in a minivan, driving along the A16 motorway. At some point they opened the door of their van and waved fake weapons at other road users. The police say they were “flooded” with calls from alarmed motorists.
Terror suspect studied in Holland The 24-year-old Omar B., who was arrested by German police last week on suspicion of planning a
terrorist attack, is a student in the Netherlands. The Somaliborn German studies technical physics at the Saxion University of Applied Sciences in Enschede, near the German border. He was arrested in Cologne by German armed police on board a KLM flight to Amsterdam only minutes before takeoff. According to the German media, the man and a 23-year-old companion were planning to travel to Pakistan. However, both suspects were released on Tuesday. According to their lawyer, a farewell-letter found in Omar B.’s appartment was actually a love letter.
Photographer Hans Stakelbeek has travelled to Afghanistan on several occasions on assignment for the Dutch Ministry of Foreign Affairs. His photos are currently on exhibition in the public library in Groningen (Oude Boteringestraat 22, second floor). According to the Ministry of Foreign Affairs, the pictures show “the country’s reconstruction, but also the country’s and its people’s long road towards peace and stability.” Open Monday – Saturday. Admission free.