Friday, 21 May 2010

Does DNA = life?

Jane Calvert and Emma Frow reflect on the Venter Institute’s breakthrough

The publication of the paper ‘Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome’ by scientists at the J. Craig Venter Institute has been accompanied by the expression of a whole spectrum of hopes and fears that we have come to associate with new biotechnologies. But we suggest that some of the more overlooked features of the paper may turn out to be the most interesting. Here we highlight four.

Synthetic vs natural
The authors of the paper are keen to stress the 'synthetic-ness' of their new cell. The word ‘synthetic’ in this context relates primarily to the fact that the genome was chemically synthesized from component DNA nucleotides in a laboratory (by the company Blue Heron Biotechnology). The sequence of genome itself is virtually identical to one found in nature (that of the bacterium Mycoplasma mycoides), and characteristics of the ‘synthetic’ cell are almost identical to the ‘natural’ M. mycoides. But it is interesting that the paper continually draws our attention to novelty of the synthetic genome compared to the ‘natural standard’. However, this natural standard is itself a strain of bacteria that has been bred over decades for use in a laboratory context. We might ask how ‘natural’ this lab strain really is.

One fascinating feature that differentiates the ‘synthetic’ from the ‘natural’ genome is the insertion of four ‘watermarks’ by the JCVI team. These apparently include a serial number, the names of scientists involved in its creation, and – it is rumoured – three quotations. The paper states that these were introduced so that the investigators could distinguish their synthetic DNA from naturally occurring DNA, and assess whether their experiment had been successful. However, other possible reasons for watermarking DNA are not mentioned in the paper. One such reason could be to mark provenance, and to trace illegitimate use. Another may be to do with patentability. It is not possible to patent a 'product of nature', so the less natural the genome is, the easier it will be to claim it as an invention.

The importance of cellular context
Some commentators have already argued that synthesising a genome is not the same as synthesising a cell, because a genome needs a cellular context to transform it from an inanimate chemical sequence into a part of a living system. Although the authors admit that their ‘synthetic cell’ does not have a synthetic cytoplasm, they say that the properties of the cell are the same as if the whole cell had been produced synthetically, because the new DNA takes over the production of all the proteins in the cell. But does this underplay the importance of cellular context? This context is still a crucially important part of the new ‘synthetic cell’ because it provides all the initial machinery for DNA replication and other essential processes.

Use of metaphor
One thing that is striking in this paper is the continual use of computational metaphors – for example, that we can store “the genetic instructions for life as a digital file”. We are also told that “the DNA software builds its own hardware,” and much of the press surrounding this paper has referred to “booting up” the recipient cell with the synthetic genome. Seeing DNA as software instructions in this way, and thinking of cells as small computers are now very familiar ideas, but we should not forget that they are metaphorical. The fact that these metaphors have become widely accepted and unproblematic is interesting in itself, but this shouldn't stop us from asking about their limitations and the assumptions that they carry with them.

The language of ‘control’ is also heavily present in the paper, which repeatedly talks about how the new cell will be ‘controlled’ by the synthetic genome. But is this the appropriate way of understanding the interaction between a genome and its cellular environment? If context-dependence and evolvability are important characteristics of living things, does the idea of ‘control’ lose some of its force?

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