JSUR? Yes, sir. (Updated 2-FEB-2010)

The most exciting phrase to hear in science, the one that heralds new
discoveries, is not ‘Eureka!’, but ‘That’s funny…’ -Isaac Asimov

Thanks to Ruchira Datta for pointing out this one.

Science is many things to many people, but any lab-rat will tell you that research is mainly long stretches of frustration, interspersed with flashes of satisfying success. The best laid schemes of mice and men gang aft agley. A scientist’s path contains leads to blind alleys more than anything else, and meticulous experimental preparation only serves to somehow mitigate the problem, if you’re lucky. This doesn’t work, that doesn’t work either and this technique worked perfectly in Dr. X’s lab, why can’t I get this to work for me?  My experiment was invalidated by my controls; my controls didn’t work the way the controls were supposed to work in the first place. I keep getting weird results from this assay. I can’t explain my latest results in any coherent way… these statements are typical of daily life in the lab.

This stumped and stymied day-to-day life is not the impression of science we get from reading a research paper, when listening to a lecture, or when watching a science documentary show. When science is actually presented, it seems that the path to discovery was carefully laid out, planned and  flawlessly executed, a far cry from the frustrating, bumbling mess that really led to the discovery. There are three chief reasons for the disparity between how research is presented, as opposed to what really goes on. First, no one wants to look like an idiot, least of all scientists whose part of their professional trappings is strutting their smarts. Second, there are only so many pages to write a paper, one hour to present a seminar or one hour for a documentary: there is no time to present all the stuff that did not work. Third, who cares about what didnt work? Science is linked to progress, not to regress. OK, you had a hard time finding this out, we sympathize and thank you for blazing the trail for the rest of us. Make a note for yourself not to go into those blind alleys that held you back for years and move on. We’re not interested in your tales of woe.

Only maybe these tales of woe should be interesting to other people. If you make your negative results public, that could help others avoid the same pitfalls you had. If you share the limits of a technique, a protocol or software then someone can avoid using it in a way that does not work. A lab’s publications are actually the tip of the sum total of its accumulated knowledge.Every lab has its own oral tradition of accumulated do’s and dont’s. Not oral in the literal sense: they may even be written down for internal use, but never published. UPDATE (2-FEB-2010): most peer-reviewed journals don’t like stuff that does not work. Thanks to Mickey Kosloff for pointing out the Journal of Negative Results in Biomedicine and The Journal of Negative Results – Ecology and Evolutionary Biology.

Until now.

The Journal of Serendipitous and Unexpected Results aims to help us examine the sunken eight-ninths of the scientific knowledge iceberg, in life science and in computer science. (So an additional field over JNRB and JNREEB). From JSUR’s homepage:

Help disseminate untapped knowledge in the Computational or Life Sciences

Can you demonstrate that:

* Technique X fails on problem Y.
* Hypothesis X can’t be proven using method Y.
* Protocol X performs poorly for task Y.
* Method X has unexpected fundamental limitations.
* While investigating X, you discovered Y.
* Model X can’t capture the behavior of phenomenon Y.
* Failure X is explained by Y.
* Assumption X doesn’t hold in domain Y.
* Event X shouldn’t happen, but it does.

The problem with the JSUR model, and the nature of discovery

I expect JSUR will be a great way to comment on  methods and techniques. Indeed it will codify a trend that has been going on for some time: public protocol knowledge sharing. Many sites like openwetwareseqanswers or the UC Davis bioinformatics wiki have been doing this for a while. Not to mention a plethora of blogs. Scientists are willing to share their experience with working protocols and procedures, and if this sharing of knowledge can be now monetized to that all-important coin of academia, the  peer-reviewed publication, all the better.

So where is the problem? The problem lies with discovery, and credit given towards it. It would be very hard to get anyone to share awkward, unexpected or yet-uninterpreted results. First, as I said, no one wants to look like an idiot. Second, unexpected or yet uninterpreted results are often viewed as a precursor to yet another avenue of exploration. A scientist would rather pursue that avenue, with the hope of  the actual meaningful discovery occurring in the lab. At most, there will be a consultation with a handful of trusted colleagues in a closed forum. If the results are made public, someone else might take the published unexpected and uninterpreted results, interpret them using complementary knowledge gained in their lab, and publish them as a bona-fide research paper. The scientist who catalyzed the research paper with his JSUR publication receives, at best, secondary credit. The story of Rosalind Franklin’s under-appreciated contribution to the discovery of the structure of DNA comes to mind. Watson and Crick used the X-ray diffraction patterns generated by Franklin to solve the three dimensional structure of the DNA molecule. Yet she was not given a co-authorship on the paper. (And she did not even make the results public, they were shared without her knowledge.) Unexpected results are viewed either as an opportunity or an embarrassment, and given the competitive nature of science, no on wants to advertise either: the first due to the fear of getting scooped, the second for fear of soiling a reputation. I expect JSUR would have a harder time filling in the odd-results niche, but I hope I am wrong.

But if you have protocols you are willing to share…what are you waiting for? Get those old lab notebooks, 00README files, forum posts  and start editing them to a paper. You are sitting on a goldmine of publishable data and you did not even realize it.

Finally, here are two scientists who never declined sharing their unexpected results.

This post has been slashdotted. Exercise extreme caution.

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3 Responses to “JSUR? Yes, sir. (Updated 2-FEB-2010)”

  1. Mickey K says:

    Great piece. A small comment though:

    “Peer-reviewed journals don’t like stuff that does not work. Until now.”

    Well, there are some precedences. For example, the Journal of Negative Results in BioMedicine
    ( http://www.jnrbm.com/ ), or the Journal of Negative Results – Ecology & Evolutionary Biology
    ( http://www.jnr-eeb.org/index.php/jnr/index ).

  2. Iddo says:

    Ha! Post updated to reflect that. Thanks.

  3. Guillaume says:

    A few add to Mickey’s comment:
    The “All Results Journal” series also publishes all kind of results (Positive or Negative)