"I'll PubMed it and find out..."

Jul 07 2008 Published by under Conduct of Science

Most of the audience for this blog will be familiar with the use of "Google" as a verb to describe searching the World Wide Web for information on a given topic. "I googled a half-dozen mojito recipes which we tried out on the Fourth". "Did you google your blind date/new postdoc to make sure he isn't a psycho?". "You got dinner plans after the conference sessions end for the day? No? Lemme google up some restaurants."
The applications of "to google" are endless and endemic. Many, if not all, readers will admit to the fact that the ability to nearly instantly seek out a large amount of data (some accurate, some not, some misleading, true) on any topic of interest has become a default part of daily life. Those of you with iPhones, well, a part of hourly life perhaps?
Lagging well behind this transformation of our information-age lives, but assuredly steaming right along behind, is the verb-ification of PubMed. For some of us, it is here already. This is the area where I am sympathetic to the antics of the Open Access Acolytes™.


A recent foofaraw (including offerings from YHN and PhysioProf) arose over an ill-advised tone struck in an attack editorial thinly veiled as an analytical news item published in Nature. The discussion has brought Open Access science [several tomes on OA linked here] back to the blog-table for discussion. I have another thought, beyond my reaction to the sneering tone of the aforementioned attack editorial. One of the ways I think the Nature piece may possibly have gone astray is in not recognizing the depth to which their customers, research scientists, are reflexively sympathetic to the notion that our product--the primary scientific observation--should be freely available to all. I have been interested to hear some perspectives on why Open Access trips the trigger from some bloggers not previously on the OA Nozdrul or wackaloon lists.
As one pertinent example, JuniorProf discussed the merits of Open Access science from the perspective of supporting the needs of scientists in developing world countries in his post on why he supports Open Access.

I got an email from a young, female scientist in Nigeria. She had trained in Belgium and decided to go back to her home country to start up her own research lab. She emailed me because she wanted to use adult trigeminal neuron cultures to address her research aims and she had some questions about the details of our protocols...she informed me that she had found many other papers on the topic (trigeminal culture) but did not have access to the majority of them (as one might imagine). The primary reason she contacted me was because she had access to our paper (for free) and she could tell from the manuscript that we would be able to help her out. ... She further informed me that she felt that we had made the correct choice in publishing in an open access journal because in many cases it was the only way that people like her in developing countries could gain access to the scientific literature.

This approach is not just limited to active scientists nor to developing countries. What about the smaller institutions in the developed world? Should not college professors from community college to the liberal arts colleges and the smaller state universities be able to teach the primary literature? To teach students to assemble all of the best and most-relevant articles on a given topic, instead of merely those they can readily access?
This is not the issue for today though. I have been reflecting on the near universal response in my household to questions which might be informed by research science. Pregnancy/childbirth/childrearing? The system is fraught with contradictory opinions, mysterious lab results paired with inadequate clinical knowledge/communication of likely risks and probabilities. Relatives, friends or neighbors a bit unnerved by some sort of "possibly malignant" observation from a primary care physician and a week(s)-away specialist appointment? Vaccination risks? The list goes on and on. Since our household features two scientists who are reasonably familiar with searching the primary literature and assembling a degree of knowledge about a topic from the literature and recent reviews, our default option is to take a few minutes to "pubmed it". Since we also enjoy remote, nearly instant access to most of the scientific literature found, because of our institutional affiliations, it takes only a little extra time to obtain the actual articles and reviews.
This pubmedding process has many benefits, for mental health if nothing else. At a simple comfort level, this can fill the time gap between the primary care observation and the date with the specialist. Clinicians don't really seem to appreciate that 4 or 7 or 10 days between some interesting ultrasound findings and the appointment with a so-called genetic counselor is agonizing for parents-to-be; merely reviewing the literature on what might be implicated is comforting. Ditto some strange bump on the skin that might possibly be cancerous. Why exactly did someone think your kid should be evaluated for ADHD or Gramma for Alzheimer's? What options might be available for treatment?
"I'll pubmed it and find out."
The ability to pubmed primary research articles is a default part of our household. Perhaps not used as extensively as the google, but certainly an important and palpable feature of our normal lives. I see no reason not to extend this benefit to everyone. Especially to the benefit of taxpayers of the US and other countries who have already paid for this information to be generated!

25 responses so far

  • Becca says:

    Generation.com has a key distinguishing characteristic... the thirst for instant informational gratification.
    Google is a beautiful thing. Pubmed is too. It's not just about peace of mind- it's a way of thinking, a new way of life (and I don't even have an ipod).
    Pubmed'ing away from the university, when I can't just click through for all the articles, has a nasty tendancy to make me very angrier than a PP talking to a right-wing whackaloon.
    Please, dear scientists, save me from a terrible ranting fate- publish OA.

  • Coturnix says:

    Whenever I talk about OA, I always make sure to stress it is not just researchers and physicians in the developing world, but also people in small colleges in the industrial world, and even high schools.
    Are bloggers more inclined to be pro-OA because we are temperamentally the "new generation" no matter what our age? Have we grown up on Open Source (especially techie bloggers)? Rooting for kids against the guys who jailed them for downloading music? Just a very anti-authoritarian bunch, used to fending off attacks from corporate media (especially political bloggers)? I don't have the answers, but would like to see someone do a study of attitudes: bloggers compared to non-bloggers.

  • juniorprof says:

    As a fellow 2 medical professional household member I find this argument quite compelling as well. There is a wealth of clinical peer reviewed research and review out there that is much more reliable than the junk you usually find on WebMD or other such websites. Just today this literature helped me discover that my knee is fubar'ed and that I need to go to a doc right about now.
    The community college, high school, etc., argument is likewise an important consideration. We should all be able to recognize that knowledge and education are power and that we can now do something about making sure that anyone that wants to can get access to our research or clinical findings. All you scientists/clinicians out there, at the very least get your stuff into PubMed Central (and do it now, its easy! and required).

  • DrugMonkey says:

    Are bloggers more inclined to be pro-OA because we are temperamentally the "new generation" no matter what our age?
    If you mean by way of comparison with non-blogging scientists I question your premise. So long as we are not talking about the difference between fervent, public advocate and generally in favor of the concept, I mean. I think that most scientists would respond "open" if asked whether they prefer their stuff be available or not- if anyone thinks differently I'd like to see some numbers.
    This is very different from the issue of whether scientists are tied into the prestige of particular journals which have their own interests in open/fee access...I doubt very much that any measurable percentage of the reason one would publish in Nature is because they charge for access to articles!

  • juniorprof says:

    This is very different from the issue of whether scientists are tied into the prestige of particular journals which have their own interests in open/fee access...I doubt very much that any measurable percentage of the reason one would publish in Nature is because they charge for access to articles!
    Very cute way to spin that one on its head. In relation to prestige, I would argue that, at least for the scientists I have spoken to about the issue, PLoS Biology (or Medicine) have rapidly become the journals of choice behind C/N/S. I would be curious to know if this generalizes to other fields?

  • NM says:

    In terms of general medical journals Plos Med is now right up there in the top 5 of clinical med. Some of my older colleagues/bosses find this surprising but they now have a very impressive and growing impact factor.
    NEJM is still waaaayyy ahead though. Eye teeth and all that.
    Back to the search issues though- Google Scholar seems to be improving and I generally prefer it to pubmed when trying a quick search for something. People who don't have access to the journals for whatever reason could just email the corresponding author of course. Ask and you shall receive (a pdf copy in reasonable time, at least in my experience).

  • BikeMonkey says:

    The community college, high school, etc., argument is likewise an important consideration. We should all be able to recognize that knowledge and education are power and that we can now do something about making sure that anyone that wants to can get access to our research or clinical findings.
    I had a very frustrating experience trying to teach a class at a smaller institution some years ago. I was trying to get the undergrads to do presentations on articles selected by their own interests- it was a nightmare because they couldn't get access to much and our timeline was quite short for various reasons. The whole PubMedCentral manuscript thing would have been a very nice thing to have back then. I'm glad for this major step forward, even if it doesn't achieve 100% coverage overnight.

  • neurolover says:

    I'm a fervent supporter of open access, especially, when, as far as I see it, the taxpayers paid for the work already. But, I think in our Nature group bashing (including the second article you linked to), we're ignoring what the publishers bring to the table about the debate. They're saying that fee/publication won't support a journal that isn't run by a volunteer staff (i.e. scientists, who are paid in other ways by their work). They argued that PLoS Biology is proving that, since it needs the subsidies (both by funders & by the open access PLoS One) in order to survive (of course, they don't say whether each of the Nature mags is self-sustaining and profitable).
    PhysioProf says *good*, journals shouldn't be run by professional editors (though a bit more colorfully). I disagree and think there's room for professional editors.
    Then, the next question is whether "ranking" of publications by journal can be preserved in an open access society and whether we think there is value to the ranking of journals.
    As I've said, I'm pretty close to being a wacky supporter of open access (I have a t-shirt that says "fair use has a posse" -- anyone else know whose slogan that is?). But, I do fear scientific publishing becoming like the blogs. Right now, people try harder (whatever that means) so that they can break into the glamormags. Those rags are part of the reason that the controls/criterion for genetic phenotyping has improved. They ask people for controls to improve their studies. If everyone just publishes in PLoS one, publishes half-finished studies, is that an improvement?
    Now, to argue the other point, I also think that people are spending so much time to publish some things in the glamor mags, that it takes far too long for publications to come out and enter the public literature. I know too many instances where essentially the same publication took years circulating through different journals before landing somewhere, because folks wanted to break into the big time.
    I do think the world is changing, and I think we do a disservice to the changing publishing world if we ignore what the people who do the publishing do, on some grounds of "for-profit evil."

  • tg says:

    regarding the title,
    i do think the syntax is more like "I'll do a pubmed..and find out.."
    🙂

  • Dan says:

    Neurolover writes: If everyone just publishes in PLoS one, publishes half-finished studies, is that an improvement?
    Oh, come on! We all know people in our field who publish half-baked articles in great journals, and people who's work, regardless of journal, is solid. If we didn't have journal rankings to fall back on then we'd have to (gasp!) value an article on the quality of the science.

  • PhysioProf says:

    PhysioProf says *good*, journals shouldn't be run by professional editors (though a bit more colorfully).

    What the fuck are you talking about? I never said anything even remotely close to that.

  • TomJoe says:

    Before Open Access even hit the scene, it was not all that uncommon to come across a reference that was not in the university library. When such situations arose, I fired off an email to the corresponding author, who in turn was usually quick to respond with a PDF or a reprint. In part, I think it's the responsibility of the scientific community to look after their own. Sure, we'll get the assholes who like to eat their young, but by and large, I think most would be willing to send out PDFs/reprints for other, less fortunate, typically new, researchers.
    I guess for me personally, OA really isn't an issue at this point and time. Working for the government, I don't have this problem. By the very nature of my position (all my work is directly funded by taxpayer dollars), all my published work is public domain ... whether Nature, Science, or any other journal for that matter, wishes it to be so. I publish, it goes on the internet immediately, freely accessible to everyone.

  • TreeFish says:

    Thanks for pulling it, DM. I hate to reveal any unnecessary details...

  • DrugMonkey says:

    Ok, here's one of the fascist hammer things about this blog, peeps. (For those that haven't been paying attention, I just deleted a couple-three comments.) Nobody did anything too horrible but I want to nip this in the bud a little bit.
    I respect people's own minute-by-minute decisions with respect to pseudonymity and anonymity. I use a pseud myself, obviously, and for well-considered reasons. I also appreciate that there is no such thing as really hiding on the net against a determined (or even against a casual) sleuthing.
    Nevertheless, my request is that you all not contribute to any speculation or outing of anybody here on this blog. I don't care if the clues are obvious, nor if the person has left a series of tracks elsewhere that have them dead to rights. The point is to not draw attention to any such clues or links such as to decrease the burden of identifying someone. If someone wants to out themselves, fine, they can go right ahead and use their real name. If they do not choose to do so, please leave it alone.
    I will note as well that there is an error rate and that you should consider the situations of any false positives as well. The false positives that have gotten back to me about who I am were pretty good humored about it but still...

  • DrugMonkey says:

    Thanks for pulling it, DM. I hate to reveal any unnecessary details...
    I myself once posted a "lookit who I found" comment awhile ago on a blog I shall not mention. So I'm not assigning any ill will here. Everyone likes to solve a puzzle. Just keep it to ourselves, eh?

  • Piled Higher, Deeper says:

    PhysioProf says *good*, journals shouldn't be run by professional editors (though a bit more colorfully).


    What the fuck are you talking about? I never said anything even remotely close to that.

    You guys switch around your Good Cop / Bad Cop schtick fast enough that we get confused! I think it was DM that was dissing the professional editors...?

  • pinus says:

    my apologies also, completely understand the bud-nipping.

  • neurolover says:

    guess I was confused. But is there a role for what the professional (and to me this means scientists w/o labs) making decisions about what gets published?
    And, if so how do we fund their work? What about the front material? Like the reviews and editorials?

  • DocDragon says:

    Junior Prof stated "In relation to prestige, I would argue that, at least for the scientists I have spoken to about the issue, PLoS Biology (or Medicine) have rapidly become the journals of choice behind C/N/S. I would be curious to know if this generalizes to other fields?"
    As someone who is not technically in the "medical" field, I must agree that a journal's impact factor has a great deal of weight when it comes to deciding a target journal for my papers. In fact, OA was never a consideration before today.
    As faculty at a small, private university, I would love access to as much data as I can possibly absorb. I would love it if all articles on all topics had OA.
    That being said, some journals in which I have published charge a fee to the authors to provide "optional OA" of the article. Since my institution is small, the extra $5,000 (approximate) per paper can not be worked into my department's budget (heck some of our computers are still running Windows 2000).
    So, we at small institutions are hurt coming and going. We must carefully pick and choose which articles we access based on affordability *and* we can not always provide our peers with OA to our findings.

  • Dr Vector says:

    I knew I was living in the future when I asked one of my students about a sudden burst of curiosity last semester and he said that he'd Wikipediaed some stuff from lecture.
    Gotta go now, I'm planning on LOLcatting my lunch hour.

  • DrugMonkey says:

    he said that he'd Wikipediaed some stuff from lecture.
    I think I misread that at first. You mean he was a Wikipedia editor and he was uploading what you said into an entry? The future indeed.
    Of course, Wikipedia entries can be full of crap at times.

  • Pinko Punko says:

    Uh, some of the lab kids these days are too lazy to even go to PubMed. They just go to google and wade through pages of crap. Also, I love Wikipedia, but again, the lazy kids.
    I have my grampa pants on tonight, cum onion belt.

  • M-DM-A says:

    DM, re: crap in wikipedia entries...take the initiative to cull the crap from the subjects you find are important for the public to know. that part does not depend on scientific funding, at least not directly.
    two respected neuroscientists in our field took over a major topic in wikipedia to set the record straight. furthermore, it makes for a better read when there are citations, which the public at large does not always use.

  • TomJoe says:

    Uh, some of the lab kids these days are too lazy to even go to PubMed. They just go to google and wade through pages of crap.
    Actually, Google Scholar comes in pretty handy. There have been times when PubMed and Scopus have let me down, only to have Google Scholar bring me right to a PDF I needed.

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