The Loom

An Open Mouse

i-7440691e8f41c730521a26e602d2cd41-mouse 25.jpgA few months ago I got in my car and drove north until I reached a remarkable building filled with several million mice. At Jackson Laboratory in Bar Harbor, Maine, scientists are studying mice to understand many mysteries of genetics and medicine. But I was particularly curious about a project that they’ve only recently launched: an attempt to understand how many genes working together give rise to complex traits. When those complex traits go awry, the result may be a common disease such as heart disease, diabetes, or cancer. The article I wrote about what I learned, “Mendel’s Mouse,” appears in the May issue of Discover. Discover posted the story today on their web site, where you can read it for free here. (I’ve also archived it here.)

Talking about this article is also a chance to add my two cents to a discussion that’s been bubbling for a few weeks: the clash between bloggers and scientific journal publishers. Last month Shelley Batts at Retrospectacle wrote a post about a paper, and included a chart that appeared in it. She promptly got a letter from Wiley, the journal’s publisher, menacing her with legal action unless she took the chart down. A long discussion then unfolded about fair use, a concept so mystical that I get a headache every time I try to figure out whether it applies to some text or image I’d like to use in my own work. Once the controversy reached Boing-Boing proportions, Wiley sent Batts a note telling her that it was all a big misunderstanding and that they “would typically grant permission on request in order to ensure that figures and extracts are properly credited.”

For us science writers, there’s a huge irony to this episode. Scientific journals like attention. The better-funded ones will go to great lengths to get stories written about their papers. They offer us science writers elaborately appointed press packages offering sneak peeks at papers coming out in the near future. They sometimes give us the cell phones of the authors of those papers, in case we need to call them in the middle of the night. They give us pretty photographs to use (as long as we fairly credit them).

But scientific journals also cling to conventions that block the news from spreading–particularly through the online world. Wiley, for example, initially reacted to Shelley not with enthusiasm, but with a menacing note. When Shelley responded by politely asking for permission, she was told to contact another person at Wiley. And when Wiley finally sort-of apologized, they still expected Shelley to jump through conventional hoops to get permission. All this kerfuffle over a little graph. It might have taken days to get permission to reprint it, which in the blogosphere is a geological era. Wiley was, consciously or unconsciously, going out of their way to squash interest in their papers.

Compare Shelley’s experience to what I’m about to do. I’m going to–shudder–reprint a diagram from a journal. Just lift it straight out. I like this diagram, because it elegantly conveys a point I tried to make in the Jackson Laboratory article, but Discover decided not to use it. So I’ll use it here.

We tend to think of traits as being controlled in a simple way by genes. One gene drives one trait. You sometimes hear people talking about the “gay gene,” the “depression gene,” and so on. But this view is almost entirely divorced from reality. The scientists at Jackson Laboratory illustrated this fact in a paper they published last summer in the journal PLOS Genetics. They looked for the genetic source of obesity in mice. They mated mice from dozens of inbred strains and then looked at later generations, meausuring variations in body weight, the size of fat pads, and other traits linked to obesity. They then pinpointed regions of the mouse genome where variations produced variations in those traits. They didn’t find an obesity gene. Instead, what they found was this:

i-33e024584bd4eea47b9d13ccaa9007f3-PLOS image.jpg

You can click on the image to go to the source, which has details about the abbreviations. But the gist of the picture is easy enough to see. Each trait is influenced by many genes, and one gene may influence more than one trait. And different traits influence each other. And those influences can be positive or negative. This, I suspect, is what genetics is going to look like in the coming century.

And what do I now hear from PLOS? Do I hear the grinding of lawyerly knives? No. I hear the blissful silence of Open Access, a slowly-spreading trend in the journal world. PLOS makes it very clear on their web site that “everything we publish is freely available online throughout the world, for you to read, download, copy, distribute, and use (with attribution) any way you wish.” No muss, no fuss. If I want to blog about this paper right now, I can grab a relevant image right now from it. In fact, I just did.

I certainly appreciate the importance of copyrights (as the owner of many for my articles and books), but in these situations, keeping information behind a thick wall starts to seem a bit crazy, like the loss of precious bodily fluids. Far from committing some sort of violation to the PLOS paper, I have actually just spread the word about it. A few readers may even go back to read the original. And it was so easy and straightforward for me to do so that I will be very reluctant to bother with anything else.

Update: 5/24: Discover link fixed.

Comments

  1. #1 GueSt
    May 24, 2007

    There is, however, one example for a single gene that is capable of changing a complex behaviour:

    http://www.nytimes.com/2005/06/03/science/03cell.html?ex=1180152000&en=f5f81fe0ac54ceac&ei=5070

    Is it the sex gene then? (It has no homolg in humans)

    The same group recently published a follow up in nature.

  2. #2 Ed Yong
    May 24, 2007

    I *love* that diagram and the build-up to it :-) It just perfectly illustrates why the discovery of a single ‘fat gene’ is completely unrealistic. I think the other common misconception about the genetic influences of obesity, for example, is that people believe that any discovered genes flip on a simple switch from ‘Obesity off’ to ‘Obesity on’. In reality, any obesity-related genes (or in fact, any depression- or gay-related genes) will probably exert their effects through very subtle behavioural changes, and this really needs to come across better in science journalism.

  3. #3 Carl Zimmer
    May 24, 2007

    GueSt [#1]: The gene you point to certainly does seem to have a major influence. However, its influence arises from controlling other genes. I wouldn’t be surprised if variations in those downstream genes have an effect on levels of aggression, etc. Also, this gene may be a relatively rare example. As I write in my article, even the color of a mouse’s fur is controlled by several genes. And major diseases appear to be controlled by many more. Single-gene diseases are pretty rare, for basic evolutionary reasons: they can be easily elminated from the population through natural selection.

  4. #4 D Fitch
    May 24, 2007

    Your link to the Discover article skips to page 3; here’s one for the start of the article.

    http://discovermagazine.com/2007/may/mendel2019s-mouse/article_view?b_start:int=0&-C=

    Fascinating writing, as per usual. Thanks!

  5. #5 Ben
    May 24, 2007

    For a humorous look at Fair Use, you might also check out the video A Fair(y) Tale by Eric Faden.

    Explains the whole issue in ten minutes of ‘fairly used’ comedy.

  6. #6 John Garrett
    May 24, 2007

    Re fair use – what publishers forget to mention is that the many abstract journals (publications which provide only abstracts of scientific articles) do so without permission of the publisher; if publishers complain, they stop publishing abstracts of their journals, eliminating a major source of publicity. A quick descent from their high horse.

  7. #7 Owlmirror
    May 24, 2007

    In addition to genetic factors in fat formation, there certainly seems to be nongenetic factors involved with obesity as well; specifically, gut bacteria population.

    PDFs of the various papers here, as well as interesting related research into symbiosis:

    http://gordonlab.wustl.edu/Publications.html

  8. #8 llewelly
    May 24, 2007

    That diagram resembles a rat’s nest.
    What idiot designed that code?

  9. #9 Allison Hawxhurst
    May 24, 2007

    Thanks for using the PLoS Genetics figure–and for your support of Open Access publishing!

    Figured I’d break the silence from PLoS to say that we always appreciate it when our content is reused. We’ve even put up a link to your post on our websites (see “No Muss/No Fuss” with the green recycle icon on PLoS Genetics).

  10. #10 Jon H
    May 25, 2007

    Oh dear, I hope some nutter doesn’t read this and decide that those mice need freeing.

  11. #11 luca
    May 25, 2007

    I also advocate free access to information, especially if publicly funded. My old university introduced such a policy, and they’ve been making available every paper published by them on their servers, as far as I know.

    As for PLOS and other such journals, I guess it’ll take some time for dubious scientists to get confident with them. If good research is published there, the Impact factor will grow quickly and more and more people will feel like trying it.

    But, how do these journals fund things such as servers, editing, and so on?

    I did review a paper once, so I know this is free of charge for them – but the reviewers do actually spend quite some time on it. Doesn’t PLOS need some permanent employee (secretary, or so) to take care of submissions, applications etc.

  12. #12 Maxine
    May 25, 2007

    Nature, and the Nature Publishing Group journals, allow up to three figures to be reproduced for free. Pedro Belatro, a bioinformaticist, has compared journal publisher policies here:
    http://blogs.nature.com/nautilus/2007/03/journals_picture_copyright_pol.html

    Luca: PLOS has a charitable endowment. Also many publishers, NPG included, encourage authors to archive into PMC and their institutional archives, without restriction. At NPG, we explain this to authors when they have a paper accepted for publication.

  13. #13 Mark Johnston
    May 25, 2007

    Yes, open access publishing is wonderful. It’s the way it should be done in the best of all possible worlds. But somebody has to pay for it. As I understand it, HHMI subsidizes the cost of publication in PLoS journals. I hope that’s sustainable, because the amount of money provided by my grants (which pays the cost of publishing my papers) doesn’t seem to be increasing.

  14. #14 Jerry D. Harris
    May 25, 2007

    Don’t get me wrong, I’m all for open access (with or without caps) and anything else that increases freedom of the spread of information, especially between scientists, but in its present incarnation, it is highly prejudicial and, for that reason, will ultimately fail — well, at least, it will ultimately severely limit the spread of some kinds of information at the expense of others.

    Having recently submitted a paper to (and gotten reject from) PLoS Biology, I noted during the whole process that PLoS strongly requested* US$2500 up front in order to make an accepted paper “open access.” I’m not really complaining about that — in the absence of revenue generated by subscriptions (or advertising…ugh, I hate to think about ads in scientific journals…!), I fully understand that they have to get the money to stay afloat while providing free access from somewhere. What I have a problem with is that not every science — I might venture (sans data) to think that most sciences — is awash with lavish grant monies with which to cover such fees. Certainly the sciences with substantial and relatively short-order scientific boons, like genetics, biotechnology, pharmacology, etc. — sciences that can benefit the tax-paying public at large in (relatively) short order — get lots of grant money, both public and private, and can much more easily cover open access fees. Most sciences, however, do not fit this mold — many sciences, such as many aspects of geoscience, most biological disciplines, much of astrophysics, etc., do not have such short-term returns — they are more about establishing the fundamentals that can be used over a much longer term to better understand the universe in which we live; only in the longer term do the economic benefits of such knowledge typically appear. But because we live in a free-market, capitalistic society, the economy itself determines where the money goes, and it by and large goes to short-term return projects. Thus, a vast number of scientists either cannot get grants (at least not large ones) or get only partial funding that has to be applied to time, equipment, etc. rather than open access fees.

    *I say “strongly request” because PLoS does state that papers won’t necessarily be rejected, or not made open access, if the authors don’t have the funds to pay the fee, which is good…but I think it’s fairly obvious what could happen to that system if it were abused too much!

    The fault is not with open access, which is a terrific concept in principle and, I suspect, practice, and not even with any one entity in particular, be they science organization, publisher, or granting agency. But it is a sad side effect of the trend toward open access that the poorest (in a financial sense) sciences will be the last to reap the benefits. Subscription-based access to journals, at least, had the benefit of leveling the playing field to a greater extent, though even there biases were apparent, and of course subscription rates were and are bizarrely exorbitant, which greatly limited access for many. I don’t pretend to have a solution; I just think that something more equitable across all sciences needs to be implemented.

  15. #15 Jonathan Eisen
    May 25, 2007

    I like that everyone seems to agree that Open Access is a good thing. Now what we need to do is to figure out the best ways to implement it so that it works for all (e.g., for poorer fields such as ecology). I think there are a few things we can all do to help make this happen

    1. Lobby the government to make OA publishing a requirement in exchange for federal funding

    2. Lobby the government to provide supplemental funds to cover the costs. This is economically reasonable since the true costs of OA publishing are lower than non OA publishing (e.g., libraries do not have to buy subscriptions, there are no fees for reuse, etc).

    3. Work with society publishers in all fields, especially the poorer ones, to switch to at least a partial OA model

    4. Stop volunteering your time to work for non OA journals. Volunteer for the OA ones. Then the costs will go down. A lot of the reason that non OA journals can be so cheap is that so many scientists review/edit for them for free.

    5. Apply to funding agencies for grants to support OA journals. Just as funding agencies support conferences, workshops and courses, they should support OA journals.

    6. Make use of institutional and other repositories through which you can place preprints even those for non OA journals. The more these are used the better.

    7. Submit to journals that have a fee waiver such as the PLoS journals when needed.

    8. Pay the OA fees if you can afford it.

    9. Make better use of OA material for blogs, courses, textbooks, etc. The more it gets used the more the funding agencies will support paying for it.

    10+. I am sure they are other things …

  16. #16 Keith
    May 28, 2007

    I wonder if increasing the transparency of how money is used would be beneficial for an OA journal? If for instance PLOS were to openly list how much money they have and how it is being spent, then other people might be able to donate or volunteer to help for areas where funding is insufficent. Another idea would be to make it easier for people to donate or volunteer in other non-monetary ways. If a lot of money was being sucked out each month for server hardware or web-design issues, perhaps people or organizations who care about OA publishing would step to the plate and offer to donate needed hardware, or help out with some of the web-design.

  17. #17 M.C.Arunan
    June 9, 2007

    Open access jounals like PLoS Biology is the only hope for university and college teachers like me in India to be still optimistic despite the the tendency of the state to withdraw from funding of public education. This, when as large as 94% of the population of the age group between 18-24 do not find a place in higher educational institution in the country.

  18. #18 Pumpkinhead
    June 12, 2007

    You sometimes hear people talking about the “gay gene,” the “depression gene,” and so on. But this view is almost entirely divorced from reality

    It seems this prominent evolutionist let a little truth seep through his dyke of ideology. I wonder if he will stick by this quote when the hordes of pink faeries descend like locusts on upon his next speaking engagement. Even if he doesn’t, this quote will surely be in the next issue of our church newsletter!

The site is currently under maintenance and will be back shortly. New comments have been disabled during this time, please check back soon.