The BioMachine

Since the discovery that RNA molecules can act as catalysts in chemical reactions, they have become prime candidates for being the kick start that life on Earth need billions of years ago. Although the conventional explanation is that proteins were cooked up in the primordial oceans and ultimately became parts of living organisms, there is no clear way to get from proteins appearing randomly to self-organising systems based on proteins.

Although proteins can make efficient catalysts, they have no clear way to reproduce. RNA is now a much more likely candidate as it can pass on genetic information and catalyse the reactions needed to do it. Although proteins are now responsible for most of the body’s catalysis, RNA ‘ribozymes’ are still in active and can be found at the heart of what are understood to be some of the most ancient cellular functions.

Amid the excitement around being able to synthesise and edit DNA directly, it's easy to forget about some of the older methods for altering a genome. Methods that are more acceptable in places such as Europe when genetic modification has an extremely bad image.

For a new breed of potatoes designed to only produce a starch suitable for treating paper as well as foodstuffs, a team at the Fraunhofer Institute in Germany used good old-fashioned breeding to get the job done. Well almost. Good old-fashioned selective breeding with the foot hard on the accelerator pedal, using directed-evolution techniques to speed up the process of producing viable variants.

There's nothing particularly new about speeding up the process. Although protesters look upon direct genetic modification as 'unnatural', it's worth noting that plant breeders have used chemical and radiation treatment for some years to induce mutations that speed up the process of moving the candidate genomes into new territory. However, because these techniques do not carry the tag 'GM', nor do they carry the stigma.

"We are working here with natural principles. In nature, sunlight triggers changes in the genome, With chemistry, we accomplish the same thing - only faster," said Jost Muth of Fraunhofer IME in the release put together by the institute.

Normally, you have to wait after a burst of cross-breeding and mutation to see what crops develop. Not in this case. As soon as the seeds germinated, samples of the leaves were taken and their genomes analysed directly to see which mutants had picked up desired traits.

The researchers analysed 2748 seedlings to find a genome that had the genetic profile they were aiming for: the ability to produce amylopectin exclusively. Luckily the potato already has an amylopectin-production gene, which reduces the amount of mutation that the potato has to go through. However, the aim was to find a mutant that could shut off the production of sister starch amylose, which the 'Tilling' potato could. This avoids the need to purify the starch after harvesting and separation.

This autumn, the team grew about 100 tonnes of potatoes with the required genome, and without specialised GM trials. "Special measures aren't necessary, because the Tilling potatoes are totally normal breeds that contain no genetically modified material," said Muth.

The name Tilling is derived from the name the team gave to the process: targeting induced local lesions in genomes, a technique developed in the late 1990s in Seattle.

The Innovation, Universities, Science and Skills Select Committee has published a set of UK government responses for its 'Evidence Check' programme on topics ranging from homeopathy to synthetic biology. Although the response from the Department of Health on the status of homeopathy in the health service is a little disconcerting, the most interesting response is from the Health and Safety Executive on possible future regulation over synthetic biology, particularly artificial cells.

The executive takes the view that most of the existing work on synthetic biology is already covered by regulations on work with recombinant DNA, which seems fair enough. However, the response adds:

"Future work may involve the creation of artificial cells, which would not fall within the scope of existing legislation. Consequently, a minor amendment is being proposed to the definition of GM as part of the development of a single regulatory framework for work with human and animal pathogens and GMOs. This will enable the regulations to cover artificial cells, should the technology develop in that direction. This change will be consulted on prior to the implementation of the new regulatory system."

The amendment for the single regulatory framework, the executive adds, is likely to extend the definition of genetic modification to include the "introduction of genetic material into a cell artificially created for that purpose, where the cell is then capable of replication or of transferring genetic material".

I can see two potential issues with this. One is what happens if the definition of artificial cell extends to bioreactors? Will that make the operation of biobreweries more difficult? And, more fundamentally, what does 'genetic material' mean in this context? Early artificial cells will doubtless use standard DNA but does the definition of gene cover synthetic nucleic acid strands, such as peptide nucleic acid or alternative 'genetic' systems based on alternative nucleic acids, or molecules with a similar function?

The synthetic biology project based at the Woodrow Wilson International Center in Washington DC has picked up two grants from the US National Science Foundation.

One grant is to support a workshop that will host EU and US researchers looking at what synthetic biology can do, if anything, for sustainability. The University of Virginia will work with the Wilson Center on organising the workshop.

The second grant is to explore how online prediction markets - which have controversially been touted as ways to predict things from terrorist attacks to financial meltdowns - can be used to tap into the public mood on synthetic biology.

"Although online prediction markets have attracted significant interest from scholars and increasing application in corporate environments, little work has been done to apply these markets to critical issues in science and technology," said David Rejeski, director of the project at the Wilson Center in a statement.

Bio-design automation and synbio tools - The Design Automation Conference (DAC), held recently in San Francisco, concentrates on electrical engineering. But there are a lot of parallels between electrical design and the current state of synthetic-biology design. Melanie Swan reports on the design-automation tools that appeared at the First Workshop on Bio-Design Automation that was held on the first day at DAC.

I missed this in June when it first turned up but you can browse BioBrick parts on your iPhone with software from OpenWetWare. It's in the App Store here.