Wednesday, June 28, 2006

Wednesday, June 14, 2006

alarmism at the Guardian

or, what the UCL Dept. of Biology was laughing about at coffee today.

The Guardian

Apparently some clever person working as a "journalist" ordered a string of 78 bases of DNA from a biotechnology firm, who did not take serious controls about the oligonucleotide that they were shipping. This development has apparently alarmed the Guardian.

The package, which contained a 78-letter sequence of DNA, which is part of one of the smallpox virus's coat protein genes, was delivered by the Royal Mail to a flat in north London. The A5-sized Jiffy bag contained a small plastic phial with a tiny blob of white gel at the bottom - the DNA. The order cost £33.08, plus an additional £7 for postage.

Dear me. Well, to put this into perspective...

the smallpox genome is 185,000 letters long,

So, let's do some math here. To get the entire genome in 78 base pair oligonucleotides would require 2372 shipments, which would cost £78,465, plus an additional £16,604 in shipping in handling.

And that would just cover the cost of the DNA. It wouldn't cover the cost of actually putting the DNA together into a smallpox virus, or the replication costs, whatever. But let's not worry about the cost here. It could be covered, I'm sure, by a determined terrorist organization.

The key sticking point would be - there would be over 2300 orders made!

Still, that sounds scary, doesn't it. The resulting genome could be used to produce smallpox, right? Well, not exactly. It seems that there were stop codons added to the code.

In order to avoid our sequence coming under the act the DNA sequence we ordered had three changes built into it to create so-called "stop codons".

These are effectively full stops in the genetic code which mean that if the sequence were ever put together with others to make a smallpox gene the protein production machinery would stop at that point. So the sequence could never form part of a functional gene.

And so the issue is...the Guardian could order a miniscule part of the smallpox genome that had already been crippled. And we should be alarmed?

Mind you, I do take the possibility of biological attacks fairly seriously. I'm still concerned about the anthrax letters mailed in 2001. But the avenue suggested by the Guardian would be fairly low on my worry list. I'm far more concerned about the security at a bioweapons lab, where a non-crippled test sample could be stolen, than I am about the possibility of some home-stiched smallpox virus.

Friday, June 09, 2006

And what is so rare as a day in June?

I remember first facing this question, posed poetically by James Lowell many years ago. My first thought was "Why, a day in April, September, or November!" Which is why my time Bloomsbury is spent crunching numbers as opposed to pursuing literary goals.

Anyway, June in London is lovely, again, as it was a year ago. The World Cup is starting shortly, I've gotten myself a headset so I can use Skype for international phone calls, and my brother is visiting in a few weeks as part of a visit to Oxford.

What else is new? Ann Coulter has seen the pale and zoomed straight beyond it, an overrated "terrorist" leader named al-Zarqawi has learned that declaring an affiliation with Al Qaeda can be a bad idea, and the NBA and NHL finals look fairly uninteresting. And I've changed the name of the blog to something a bit less obscure.