When did announcing science become the same as publishing science?

When I was a postdoc, I used to make a Friday morning ritual of browsing through the latest issue of Science while drinking my coffee and listening to one of my favorite music podcasts. It was one of the highlights of my week, but that ritual has been long since buried by the simple fact that I just don't have time during the day to casually read through a whole journal.

But this morning, I tried. I didn't get all that far, however, because one item in the News of the Week section caught my attention and sent me looking around at other sources as well. Maybe I have just been oblivious to the subject of the article because it is not my game, but I nevertheless found the piece on Stephan Schuster getting "scooped" in his efforts to sequence the genomes of both the cacao tree and the Tasmanian devil. Why this article was so interesting is all in the nature of the scooping.

When I think of getting scooped, it means that another lab has published the major findings of something I am working on before my group was able to get the paper out. I don't think I am alone in that definition, though I haven't checked Urban Dictionary. Instead, Schuster was "scooped" because two other labs announced that they had sequenced these genomes. Uh, okay. So fucking what? According to the article, this is a devastating blow to Schuster's group, even though they have the cacao paper submitted and they are already analyzing the Tasmanian devil sequence. My guess is that they are significantly ahead of both rivals at this stage and will get their papers out first, so why is this a big deal? Science quotes Schuster as saying:

"With what happened yesterday, I don't believe in scientific publication anymore," says Schuster, who thinks work shouldn't be publicized until after peer review. "We tried to be a good citizen, ... and we lost."

You lost? What? Okay, okay, I can see how the initial big publicity would have been cool and all, but aside from a very small circle of people, who is going to remember which group made the announcement? No one. Most people will remember hearing that an announcement was made and then see the paper in a month or two and say "Hey, that chocolate genome is out. Cool." Schuster's group will get the citations and the other groups will be forced to publish their results in a less GlamorEleventy!!! journal and run all the comparative analysis. I guess I'm missing where Schuster "loses" here, unless this has more to do with the initial round of applause than anything else. In fact, they even get to be smug about how much further ahead they are:

The Penn State-CIRAD group sequenced the Criollo variety of cacao, assembling 76% of the cacao genome into its 10 chromosomes and placing 82% of the 28,798 genes along this DNA. "We were at the point of the [Mars-USDA] press release about 6 months ago," claims Guiltinan.

What also seems ridiculous to me is that there are TWO groups sequencing either of these genomes. I can understand the race for the human genome and maybe even things like fruit fly and Arabidopsis, but since when did the Tasmanian devil fan club go all cut throat? And I like chocolate as much as the next person, but two genome sequences*? It's hard to tell whether this is competition or lack of communication, but either way it seems like a giant FAIL to commit the duplicated resources. If it's the former it's just stupid and if the latter maybe it's time to think about a mechanism by which people could list what genomes are being sequenced (and not in a something-I-want-to-do-one-day-and-this-is-a-way-to-pee-on-it, kinda way. Things actually on the machine.).

We also see the whole making data public before it is analyzed thing raise it's head again.

While Schuster was fretting about his group's Tasmanian devil work being overshadowed, his colleagues working on the cacao genome were scrambling to prevent the same thing from happening to their project. The rival Mars-USDA collaboration announced that it had assembled the sequence and opened a Web site to provide other researchers access to the data.

It's one thing to have your own data released to the public right after assembly, but this is someone else's data from the same organism being put out there like a Vegas buffet. I can see this being an issue, but if you are way down the road on the analysis end, don't these announcements just light a fire to get the paper out ASAP? Statements like the one by Schuster above, might be warranted if the other groups published the data ahead of their group, but if anything, doesn't the announcement just add some buzz to the publication?

Let's wait for the papers before we start the pouting, no?

*BTW, the fact that Mars was a partner in the chocolate genome project (the second one) is something I find hilarious. Mmmmmm genom-nom-nom. Alright, maybe it's just me.

24 responses so far

  • CoR says:

    The problem, really, is that these sequencing efforts still result in big woo-hoo papers. When that ceases then the press releases should die down. At the very least, I hope the two groups are at least sequencing different varieties of cacoa so comparative work can be done. And yeah, Phillip Morris is sequencing tobacco. Company cash.

  • Odyssey says:

    I blame Pons and Fleischmann for starting the trend of publishing via press release.

  • chall says:

    well, he might have been scared of getting scooped by two groups at the same time... although, as you state - his paper is in review/submitted? And isn't this sequencing stuff getting to that point you mentioned in an earlier post - is it sequencing, assembling or analysing the sequences that should give the publication? \

    (I'm the first to admit that sequencing is messy and not easy, but at the same time I'm not sure that it is 'more' than a technique... it's the results from the analysis that is interesting, non?)

    As for the cacao, it's expensive... and my guess is that they want to see if they can improve, or find markers for taste ;) Or, which might be more likely, establish what "kind" it is genetically, once you have a sample you want to buy.

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  • hydropsyche says:

    I imagine sequencing the Tasmanian Devil genome has something to do with trying to save them from devil facial tumor disease. My understanding is that one reason the disease is spreading so quickly and is so likely to cause extinction is that the population is very small and there is not much genetic diversity among the devils, such that it's highly unlikely that any devil is immune to or is able to fight off the disease.

  • proflikesubstance says:

    Because genome sequence = disease cure, in which organisms so far?

    I have no doubt that their status has pushed this genome project forward, but remember when the human genome was going to bring us the cure for cancer? Remember when the cancer genome was going to do that?

  • ... this is someone else’s data from the same organism being put out there like a Vegas buffet.

    And exactly what is the problem with that? It's not like they put HIS data on the web. They put their own data on the web.

    Are they supposed to not make data available because someone, somewhere else, might be doing the same thing?

    Schuster is sounding like a big 'ol crybaby. Sack up and publish already!

  • proflikesubstance says:

    I wasn't suggesting that there was anything wrong with this, simply that it was a topic discussed here recently and that it would be something one could plan for if it was your own data, but might catch one off-guard in this situation.

  • ... genome sequence = disease cure ...

    There are known HLA types in which people who are infected with HIV never progress to AIDS, or progress at a much slower rate.

  • Great post! I just found your blog today and after reading a couple of posts I will be subscribing to your feed.

  • I have no sympathy for Schuster. He's in the game, and he knows how things work. How they've almost always worked! If he and his coworkers got caught off-guard it's their own damn fault.

  • With a small genetic pool, which the Tasmanian Devil suffers from, I believe finding the elements responsible for the rapid onset and propagation of this virus would have a better chance of success. The human genetic pool is much more dilute, and "the cure for cancer" is such a nebulous term ... what cancer are we trying to cure? The National Cancer Institute has a ridiculously long list of the types of cancer.

  • Maybe the real solution to the problem is modernizing the publication process so it does not take 12-18 months for research to be published. In my mind in the world of medicine, that represents 12-18 months of potentially helpful information for my patients being withheld from the medical community due to an archaic, inefficient and imperfect process.

  • What, sequencing cancer genomes hasn't cured cancer yet?! It's been, like, three whole years - WTF??!!

    /snark

    I know what you're saying, but I'd say genome sequencing is a necessary but not sufficient condition for better treatments (no-one I know talks about cures). And while some cancer types are likely to have recurrent mutations in a single gene or pathway, others are characterised by genomic instability and have much messier, noisier genomes, meaning that you have to sequence many different cases in order to find patterns: the International Cancer Genome Consortium has settled on 500 cases of each tumour type as a good starting point.

    Some of the PIs I work with were involved in this study, being touted as the first case report of truly personalised cancer treatment - they used next gen sequencing to ID a mutation in a tumour that had become resistant to first line therapy, and gave the patient a new treatment based on that discovery. This choice of treatment stabilised the disease for several months.

    So, no cure, but I'd be reluctant to dismiss the whole field this soon... and hopefully the Tasmanian devils will get lucky and have the single gene/pathway kind of cancer, where you need to sequence far fewer cases.

  • proflikesubstance says:

    I knew someone was going to come along with 345 caveats. My point was that genome sequences have been touted as the key to unlocking the secrets to XXXX disease roughly 183490u482nvjskb937u4082ut times. I don't recall a single instance where the original justification (when hung on XXXX disease) ever came to fruition. I am not at all claiming that genomics doesn't provide enormous scientific benefits, only that it is never as simple as it seems to be drawn up in the initial hand waving that gets the project funded.

  • [...] This post was mentioned on Twitter by Bora Zivkovic, Christie and Squillo, R. R said: ♻ @BoraZ: When did announcing science become the same as publishing science? http://bit.ly/dbZ8EM [...]

  • John Hawks says:

    The Tasmanian Devil represents one of the more divergent mammalian clades that hasn't yet been sequenced.

    It's a target of interest for that reason, although it's possible that the attention to DFTD risk has pushed it farther along than other clades of equal or greater depth.

  • [...] When did announcing science become the same as publishing science? [...]

  • "What also seems ridiculous to me is that there are TWO groups sequencing either of these genomes. I can understand the race for the human genome and maybe even things like fruit fly and Arabidopsis, but since when did the Tasmanian devil fan club go all cut throat? And I like chocolate as much as the next person, but two genome sequences*?"

    Does anyone know why this happened? Did Mars want proprietary access or something? Or maybe Schuster was taking too long?

    I can't believe that the funders are happy with the duplication of effort.

  • Did Mars want proprietary access or something?

    Don't know, but their data is already on the web complements of USDA-ARS. That makes me think the answer to the question is probably "No."

    http://www.cacaogenomedb.org/

  • proflikesubstance says:

    I'm a bit confused by the effort duplication as well. I would think that these circles are small enough that one would know if another group was doing the same genome, but maybe not if there is so much competition. It may just be that both were initiated around the same time and each group was either too stubborn or felt they already had too much invested to back down.

  • antipodean says:

    Luckily most of this stuff has absolutely zero clinical applicability and never will. The clinical journals will publish faster in many cases via online early view (and you can request additional rapid publication if you think what you've done will change practice immediately).

  • [...] was minding my own bloggy business the other day and ran across a link at the John Hawks weblog to the discussion we were having the other day about press announcements pre-empting publishing. While reading, I [...]

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