Data Archiving – Bird Flu

David Stockwell has an interesting post on the lack of public archiving of bird flu sequences, drawing on a longer post by Declan Butler.

So apparently, noone is opposed to depositing the sequences in Genbank immediately, but noone is taking the decision to do so. In the Nature editorial, Dreams of flu data we argued:
Genetic data are also lacking. When samples are sequenced, the results are usually either restricted by governments or kept private to an old-boy network of researchers linked to the WHO, the US Centers for Disease Control and Prevention, and the FAO. This is a far cry from the Human Genome Project, in which all the data were placed in the public domain 24 hours after sequencing. Many scientists and organizations are also hoarding sequence data, often for years, so they can be the first to publish in academic journals. With the world facing a possible pandemic, such practices are wholly unacceptable. Nature and its associated journals are not alone in supporting the rapid prior exposure of data when there are acute public-health necessities.

Lonnie Thompson is much closer to 24 years than 24 hours for not archiving his (still unarchived other than a miniscule summary) Dunde data. The bird flu data hoarders are neophytes in comparison. Let’s see if their data is still unarchived in 2025 – otherwise climate scientists will be unimpressed with such amateur data hoarding.


15 Comments

  1. Posted Jun 20, 2006 at 12:04 AM | Permalink

    I suppose the figures should ve gone down as the President Bush was planning to bombard the canary islands………. to reduce the spreading of bird flu.

  2. Jean S
    Posted Jun 20, 2006 at 3:45 AM | Permalink

    re #1: Paulcarter, could you keep these “funny” anti-Bush jokes etc in other sites, your post has nothing to do with data archieving. I’m sure, e.g., RealClimate, is happy to include comments like that. Here, however, we try to discuss actually some science.

  3. Max
    Posted Jun 20, 2006 at 4:43 AM | Permalink

    “The World facing a possible pandemic”???

    Very unlikely and I think this whole bird-flu business is greatly over blown. I have lived through the “invasion” of Europe by the Bird-flu which primarily hit poor people countries, who coudn’t afford a good standard of hygenie. So, it was neither a pandemic, nor even a grave danger.
    Some ill ducks and swans are no evidence for a dangerous pandemic, especially since there were no massive consequences. Most of the cases of “bird-flu” transmitted on humans are at least dubious.
    When a friend of mine called in Turkey to get confirmations about the bird-flu killing three men, the hospital doctor said he couldn’t release the information, but he shouldn’t worry.

    So, imo, we will never have a pandemic.

  4. Posted Jun 20, 2006 at 7:15 AM | Permalink

    #3: Your quote was taken from a quote in the post by Majikthise which is an interesting if left-leaning site. My post is meant to make the point that sharing data is not just an academic exercise.

    Still, 11 out of 16 known human cases have bird flu have died so the lethality is high. I did state that the threat is currently to poulty farmers and wildlife. That would change though if it became human-to-human transmissible, which is the concern with the Indonesian cluster. Still, I attach the rider that I am not an MD or an expert in this area.

  5. Posted Jun 20, 2006 at 8:09 AM | Permalink

    Correction — 227 confirmed cases of bird flu and 129 deaths worldwide as of 16th June 2006 (Reuters).

  6. TCO
    Posted Jun 20, 2006 at 8:26 AM | Permalink

    Messed up sidebar is still not owworking. This is really unsat for a computer consultant to product a product like this that is worse than what most hobbyists can put together and the endless blathering and amazement that people are actually looking at this site on the web (not RSS) and are using that little known program Internet Explorer from that niche company Mcirosoft just amazes me.

  7. Steve Sadlov
    Posted Jun 20, 2006 at 8:42 AM | Permalink

    Are there concerns that if the sequences were posted, less-than-nice folks would use them for illegal things in violation of certain treaties? Or is it more just ego stuff?

  8. Posted Jun 20, 2006 at 8:49 AM | Permalink

    Re:7 From Majikthise who was writing about this in October last year:

    … the CDC is assuming that they will get more innovation out of vaccine manufacturers by creating a taxpayer-funded monopoly on flu data. (Bush-bashing deleted)

  9. John A
    Posted Jun 20, 2006 at 9:14 AM | Permalink

    I’ll try to monitor the situation from the incredibly buggy and insecure Internet Explorer, which were it not artificially spot-welded to the current monopoly operating system, would have been junked long ago in favor of much better written software.

  10. BradH
    Posted Jun 20, 2006 at 6:56 PM | Permalink

    I think there is legitimate reasons for not publicising certain information which may be “weaponised”, even if the likelihood rises to no more than a “reasonable possibility”. Whether or not bird flu sequences could rise to such a standard is to my mind debateable, but then I am no expert in such matters.

    In any event, such “public interest” arguments need to be well supported, because the matter can turn on the head of a pin – indeed, if it cannot reasonably be used by the bad guys, it is distinctly against the public interest to withhold such information, because it may delay development of treatments.

  11. Posted Jun 20, 2006 at 8:00 PM | Permalink

    Re: 10. Yes I agree. I doubt the ability of H5N1 to be weaponized. I doubt it has a stable phase like anthrax. Was someone using that as a justification for withholding the sequence data? I also think there are grounds for limited or temporary rights to public-funded data. The issue of rights to data is fairly nuanced and I think that was the point that John Hunter has been trying to make. There is no justification for sitting on tree-ring data for a generation though.

  12. Posted Jun 21, 2006 at 1:55 AM | Permalink

    If i m not wrong Jean, even David is talking of figures here…..Nways….

    Whatever may be the figures, hardly matters.
    ……the threat is basically to poultry farmers and who coud’nt afford a hygeinic living. The world is under a “DANGER” undoubtedly.

  13. Posted Aug 8, 2006 at 6:44 AM | Permalink

    Is there any cure for Bird flu?

  14. john lichtenstein
    Posted Aug 8, 2006 at 10:08 PM | Permalink

    Spiced ham is not a cure for flu.

  15. Dave Dardinger
    Posted Aug 8, 2006 at 11:44 PM | Permalink

    How about clipped wings as a cure for Bird Flew?

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