An Oxford graduate student by day and a scientific activist by night, Nick Anthis isn't letting his Ph.D. research in protein structure get in the way of defending scientific and social progress.
Although Steinn Sigurdsson of Dynamics of Cats beat me to this one, I still thought I would chime in. The Guardian reports today that is was recently able to purchase a 78-nucleotide sequence of DNA based on the small pox genome and that it was able to get the supplier to mail it to a residential address. The article is alarmist and sensational, but it raises an issue that in general has probably not been given enough thought.
As The Guardian points out, it would be very difficult to reconstruct the 185,000-base pair genome of small pox from such small pieces of DNA, and the closest scientists have come to such a feat is reconstructing the 7,741-base pair genome of polio virus from similarly small pieces of DNA. Although the idea of reconstructing the much larger smallpox genome would be a logistical nightmare, it would theoretically be possible.
What is disturbing about The Guardian's report is the response of the company who sold the DNA:
Alan Volkers, chairman of VH Bio Ltd said the company had no idea that the sequence they produced was a modified sequence of smallpox DNA.The DNA The Guardian purchased had been "modified", but these modifications only consisted of the addition of three stop codons. This in particular would not be a huge roadblock, since a laboratory scientist could correct those mutations in a matter of days.He added that many of its regular customers carry out research which requires supplies of DNA sequences from pathogenic organisms, and his company does not normally screen DNA orders less than 100 letters long. After discovering that it had supplied a small sequence of smallpox DNA, the company carried out checks on two European databases and a 30-minute check using scanning software, but none of them raised any alert.
Dr Volkers added that the company processes several hundred short-sequence orders per day and added: "It would be impossible to run them all through [standard scanning software] and operate successfully."
"There are no regulations in place which require us to carry out background checks on potential customers," he said. "We will, of course, comply with any regulations which are introduced."
Although I'm reluctant to call for more government regulation on the basic sciences, I think this is one area where the potential consequences are severe enough to warrant the requirement of at least knowing and keeping track of who is purchasing such DNA sequences.
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Comments
So how much does 1/2000th of the smallpox virus DNA cost? Computer time is basically free now. I mean, you want email, right? And Windows means you need at least a GIPS machine to get it. So reassembly is nothing. It seems that the feasibility study is complete, for someone. And maybe somone could get the cowpox sequence cheaper, and fill in smallpox where it matters. That might cut off an audit trail, too. The expensive stuff would be that required to go from the genome to creating a new virus. I've no idea what that is, but it has been done for another virus.
If The Guardian (and others) posted their bits on the internet, perhaps Google could be used to get all of it. That'd be fair, since then everyone would have it.
Perhaps if someone actually creates smallpox from just the DNA information, then we could get rid of the remaining smallpox in deep freeze. It might be safer, and cheaper.
Posted by: Stephen Uitti | June 20, 2006 12:12 PM
The Guardian paid 33 GBP (just over $60) for its seventy-eight nucleotide segment, which is about a standard rate for commercially-synthesized DNA. Although that's not too expensive, the price really adds up when you consider that you would have to purchase at least 2,372 of these pieces of DNA (bringing the price up to about $190,000. You would actually need more than this, because you would need some overlap between each of the segments. The main difficulty and expense, though, would come from piecing together the various segments of DNA, which would be incredibly time-consuming and tedious. Therefore, I don't think anyone will be constructing the smallpox genome any time soon. Still, I don't think it would be unreasonable to at least track who is ordering such sequences (although I don't think it would be necessary to go any further than that).
Posted by: Nick Anthis | June 20, 2006 3:00 PM