All entries for August 2007

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

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

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…

August 2007

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