September 12, 2007

Not a good day

DEFRA has confirmed what nobody wanted to hear – foot and mouth has struck in Surrey again. The BBC were reporting it a while before the official announcement came, but I guess they have better spies than I do!

The new case is about 10 miles from Pirbright, some distance from the cases we saw in August. The strain is, as yet, unknown, but I think the assumption until proven otherwise must be that this will be the same O1 BFS67 strain that leaked from the Pirbright site to cause the earlier outbreak. The HSE’s final report into biosecurity at Pirbright makes for uncomfortable reading – while we will never know which of the three facilities on-site leaked the virus, it seems that there were several significant failings in the category 4 biosecurity arrangements on that site which combined with heavy flooding to cause the outbreak.

What’s got me scratching my head is the time-lag before this outbreak; indeed, when I heard this morning there was a suspect case, I was assuming it would turn out not to be confirmed. FMDV (the virus that causes foot and mouth) doesn’t survive for long in the environment, so why has this case appeared now, given the last infected animals were culled on the 9th of August? The OIE’s handy summary gives 14 days as the upper end of the incubation period. It can survive in the environment if conditions are suitable for up to a month, but the previous infectious premises will have been rigorously disinfected.

I think that means that direct transmission from the August infectious premises is fairly unlikely to be the cause of this outbreak. I can’t find another more plausible hypothesis, though; did more contaminated soil leave Pirbright during the recent past (surely not, biosecurity was substantially tightened up during the HSE investigation)? are there other infectious animals out there that we haven’t spotted (again, this new case is only just outside the old surveillance zone, so animals nearby would have been inspected regularly)? Even if it is direct transmission from the previous infected farms, how did the virus escape disinfection? At this stage, we will have to wait and see. Easier to do as an epidemiologist than as a farmer, trying to get back on track after the previous round of movement restrictions…


August 29, 2007

Open Access Publishing

The question of where to publish the results of research (especially publically-funded research) has been steadily coming to prominence this year, particularly following a Nature news article revealing that a consortium of scientific publishers has hired a “pit bull” (Nature’s term, not mine) of Public Relations to fight their corner. The result seems to be PRISM, a lobby group opposed to open-access publishing.

A lot of electrons have been spilled over this issue, and, sadly, it is apparant that the debate is far from well-tempered. Scientists in favour of open access publishing are angered by claims that open access would mean the end of peer review. Those claims, it seems to me, are almost entirely unfounded; it seems to me that this is a claim being put around in the knowledge that it is false, to try and scare people off open access publishing. Open access journals such as BioMed Central and The Public Library of Science Journals are peer-reviewed by scientists in the relevant field (who do so for free) in the same way that pay-to-read journals are.

The case for public access to research the public is funding (through taxation) has been made elsewhere, and debated at length, so I won’t go into that here. I think there’s a slightly different point to be made from the point of view of advancing science, though. As a scientist, it’s very frustrating to find an interesting article referenced in a piece of research I read, or that crops up when doing a literature search, only to find that my institution doesn’t subscribe to the relevant journal. It’s obvious that making my research freely available is more useful to the scientific community at large than publishing it in a journal that requires other scientists (or their employers) to pay to read it. I’m aware of the parallel here to some of the things I said about free software a while back!

For junior scientists, there’s another issue, too. The next job (particularly if it’s a faculty/tenured post) will largely depend upon your publication record. The impact factors of open access journals are often not that high (partly because they’re relatively new), which may mean that potential employers who are too focussed on bibliometrics will rate papers therein less highly. Nailing your colours to either side of such debates can be dangerous, too, if you’re un-tenured. I’m evidently not entirely risk-averse!


August 20, 2007

Podcasting on FMD

Writing about web page http://www2.warwick.ac.uk/newsandevents/audio/?podcastItem=footandmouth.mp3

Last week I was interviewed about foot and mouth disease (and my research, which doesn’t address foot and mouth specifically, but rather looks at the impact of livestock movements on the dynamics of farm animal diseases more generally) by Tom Abbott of the Communications Office.

I find I tend to “dry up” the moment someone points a microphone (or, worse, a camera) at me, but I think the interview went reasonably well, and it helped that Tom had done his homework about the current outbreak. In any case, you can hear the edited result here. It’s always a bit odd hearing your own voice played back to you!


August 08, 2007

Foot and Mouth: a second confirmed case, and the HSE's initial report

Writing about web page http://www.hse.gov.uk/news/archive/07aug/pirbright.htm

DEFRA have confirmed that a second farm has been culled, and foot and mouth disease confirmed. The second farm is within the original Protection Zone, so this doesn’t represent a significant geographic spread. There’s an interesting question as to whether this is another primary case, or whether it was infected by the first farm. It may never be possible to answer this unambiguously, but everyone will be hoping it’s another primary case, as that would mean that there have been no secondary cases so far still. This would be good, as it would mean that the current containment policies appear to be working.

The Health and Safety Executive has published its initial report on the suspected biosecurity breaches at the Pirbright site. I noted yesterday that Pirbright was the likely source of this outbreak, and I’m a little disappointed to note that the HSE report doesn’t tell us much more than what we already knew or could surmise. It rules out airborne spread as a “negligible likelihood”. The likelihood of waterborne spread is also assessed to be “negligable”, although further investigations are being carried out.

That leaves human movement as “a real possibility”. Again, further investigations are being carried out. That would be embarrasing if it were shown to be the case! The tabloids have been making much of the HSE’s failure to rule out deliberate sabotage, but that seems unlikely to me: if you wanted to release FMD, you wouldn’t pick a bit of Surrey that’s only lightly populated by livestock farms to do it in, and you’d pick a time of year when there were more movements of animals going on. Hopefully we’ll actually have some useful findings from the HSE in due course…


August 06, 2007

Foot and Mouth in Surrey

I’ve just got back from the Society for Mathematical Biology annual meeting in San Jose; my colleagues and I were a little concerned to hear of a confirmed outbreak of foot and mouth disease (FMD) on a farm in Surrey last Friday.

It’s too early to say for definite how this outbreak will pan out, but a few things can be noted now. Firstly, the government moved quickly – following initial reports, a temporary restriction zone (1km) was put in place at around noon on Friday, and by 9pm FMD had been confirmed, and movements of susceptible cattle halted nation-wide. This is marked contrast to previous epidemics in 1951,1967, and 2001, when (as noted by the enquiries that followed each outbreak) movement restrictions were not put in place rapidly enough, which made those outbreaks considerably worse than they might otherwise have been.

There is no sign as yet of secondary cases, which is positive (although given a normal latent period of 3-6 days, we cannot be sure that there won’t be some still to come); we don’t have much live data to go on as yet, but given movement data from previous years and the local geography, spread outside the current 10km Surveillance Zone seems unlikely. I hope I don’t end up eating my words…!

The strain isolated from the culled animals is very similar to the 1967 epidemic’s strain, which isn’t thought to be currently “at large”, raising the question of where it came from. The nearby laboratory site at Pirbright seems a likely candidate, althought that has yet to be confirmed. The Institute for Animal Health, the world reference laboratory for FMD (amongst other things!) is on that site, as is Merial’s FMD vaccine manufacture plant. Both have 1967-strain FMDV, the latter in rather larger quantities than the former. Both have strict biosecurity controls; it will be interesting to see the results of the HSE’s investigation, due tomorrow.

In the mean time, we can just wait and see what unfolds. Interesting times…


July 05, 2007

Free software and science

Writing about web page http://www.gnu.org/philosophy/

This might sound like a rather unpromising title for a blog post by a veterinary epidemiologist, but I think the issues surrounding free software are relevant for all of us who use computers to do science. The question of whether to use free software or proprietary software is particularly acute for modellers, and other people whose published work contains the output of computer programs.

Free software means more than just software you don’t pay for. The classic analogy is that it’s free as in “free speech”, rather than just as in “free beer”. Specifically, free software gives its users four key freedoms:

  1. The freedom to use the software for any purpose
  2. The freedom to share the software with others
  3. The freedom to study the workings of the software
  4. The freedom to improve the software, and share those improvements with others

The latter two are particularly relevant to science. If I want to validate the results of your study, a good way would be to inspect the software you used to generate those results; not simply that given the same inputs, it produces the same outputs, but that the methods it uses to generate those outputs are correct. It’s very easy to get odd corner-cases wrong, and those mistakes might go otherwise un-noticed. Even if they don’t affect the study’s findings, they might be worth fixing before doing any further work!

Science is, at its best, about a community of scholars working to improve our understanding of the world. If scientists use free software, and make it available along with their research findings, then other scientists can build upon their work, avoid unnecessary reduplication of effort, and collaborate more effectively. It seems to me that free software should be the gold standard for scientific computing. If you write software as part of your research, please consider releasing it to the scientific community under a free licence such as the GNU GPL; if you are considering what software to use for a particular research project, consider carefully if there is a piece of free software you could use (with modifications if necessary). Not because you’ll spend less of your grant on software costs, but because it’s the moral and socially responsible thing to do!


June 29, 2007

Smoking Ban

On Sunday, smoking in public enclosed spaces will be banned. I think this is an excellent thing, and will doubtless reduce cancer due to passive smoking. Still, the requirement to put signs up all over the place is a bit daft. I found the following on the internet, and put it on my office door…


May 16, 2007

Conference travel

One of the joys of academic life is going to conferences. Organising committees tend to pick pleasant bits of the world, and your grant will usually fly you there and back, and pay for the conference hotel. Sometimes you can even use a bit of holiday time up while you’re out there! I’ll elide for a moment the fact that the hotel is often in a rather out-of-the-way place, you usually have to pay for your own food and drink, and that your grant won’t pay for your spouse to join you…

Recently, I went to a conference in Corfu, where I presented a poster about some of the work I did for my PhD (if you’re interested, an A4 version for you to print out and put on your wall is here. ). These days, however, you can’t take a poster tube into the cabin with you, as it’s a security risk (so they say). I slightly nervously committed it to the plane’s hold, and hoped it would make it to the other end. It did, and was quite well received at the conference.

Getting it home again was another matter; my poster tube eventually popped out of the “outsize baggage” claim at LHR, with part of the lid missing (which means the label with my address was gone, and that it’ll no longer keep water out). So, I queue at the euphemistically-named “baggage enquiries point”, and a slightly confused lady fights with their tickybox-system which has not category for poster-tubes. Eventually, she fills out a form in triplicate, and attaches a note explaining what the item actually is. Someone will be in touch in the next couple of days, she says, and they will arrange someone to come and inspect the damage and to decide on repair or replacement.

That seems a lot of effort for a £35 poster tube, but hey. Anyhow, in due course I phone them back to inquire what’s going on, and explain everything again to someone who seems unable to find my records from the first time round. She says someone will call within a fortnight to arrange to come and look at it. Yesterday at work, I get a call “Err, was anyone at home this afternoon?” “No.” “Oh. When could you be around?”. So, this morning, I worked from home until there was a knock at the door, and a cheery man says “I’ve got a case for you”. I look at his large box, and say. “I don’t think that’s right”. I show him the damaged poster tube and observe that it’s unlikely to be packaged up in a box the size he’s put down in my porch.

He opens his box and confirms that it was a large suitcase they were trying to deliver. He makes a note, is very apologetic, and departs.

I wonder when I’ll get my new poster tube? I also wonder whether it wouldn’t have just been easier for them to let me replace it myself and send them the bill!


February 08, 2007

Avoid non–essential journeys

It’s snowing this morning, and has snowed quite a lot overnight (I estimate about two inches, from what I had to scrape off my car this morning). As is traditional in the circumstances, much of the UK’s transport network has ground to a halt. On the plus side, it meant I got a space in the free car park this morning! I don’t usually drive to work at all, but I’m going to Stratford this evening, so needed the car.

Last night, the usual motoring organisations were saying what they always say when significant snow is forecast: “avoid non-essential journeys”. Given it’s a working day, that seems foolish – most people will be out and about anyway, trying to get to work, and public transport will be worse than usual (elsewhere they seem to be able to run trains when it snows, but not in Britain…). What would be better is if they provided advice about driving in the snow: start in 2nd gear not first, leave extra stopping distance, avoid sudden accelleration or braking, etc. Mostly common sense, but it’ll be some time since most UK drivers last drove through any amount of snow, and a reminder would be more use than “don’t bother trying to get to work”!


February 06, 2007

At least the computer is working…

My desktop machine has been running flat-out all day doing some simulations for me (I hope it’ll be done by tomorrow!), which has given me a chance to catch up a bit on administrative matters. The result of which is that I now have a page in the group house-style, which you can find here. It has a little about my research interests, as well as abstracts of my publications so far. Also there is an essay on Questionnaire design. Feel free to point people at it if they send you badly-designed surveys!

As an aside, there’s a solitary duck on the pond outside my office which is quacking its little heart out, for no readily apparant reason. Any zoologists out there care to comment?


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