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JSUR is accepting submissions

March 10th, 2010 No comments

I have written about the Journal of Serendipitous and Unexpected Results before and now this just popped in my inbox from JSUR’s Google group. Apparently JSUR is now open for business.

JSUR Call for Participation

Submit your short (2-4page) and full length manuscripts to the Journal
of Serendipitous and Unexpected Results.

Over the past month we’ve received a great amount of press and
publicity for the Journal of Serendipitous and Unexpected Results
(JSUR). Thanks to everyone who helped spread the word, please keep it
up!

In Richard Feynman’s 1966 Nobel Lecture, he said, “We have a habit in
writing articles published in scientific journals to make the work as
finished as possible, to cover up all the tracks, to not worry about
the blind alleys or describe how you had the wrong idea first, and so
on. So there isn’t any place to publish, in a dignified manner, what
you actually did in order to do the work.”

We’re writing to invite you to solicit short (2-4page) and full length
submissions to JSUR.  Why not prepare a 2-4 page writeup discussing
side-investigations, alleyways, or false-starts in your latest
published or unpublished research? Papers of this length place a
minimal burden on the authors, while providing extremely valuable
research insights to a broad audience.

Journal website: http://www.jsur.org

Sincerely,
The JSUR Editorial Board

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

January 31st, 2010 3 comments

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.


Weekly poll: favorite wolf metric?

October 19th, 2009 No comments

One aspect of living in any kind of social setting is being assessed, rated and tested by one’s peers. Constantly. We are social creatures: we need to know who we are up against in any given setting. It is, after all, a matter of life and death, or at the very  of gene dispersal. We have replaced butt-sniffing, teeth baring and chest drumming with “..the firm handshake / A certain look in the eye, and an easy smile” for first impressions. (Although I would personally take butt-sniffing over certain club ties most days.)

But we do not only look for first impressions. We look for long-lasting impressions, we want to see the future. Our future of course, but also the future of our kith and kin. After all, our kin carry some of the genes we are imbued to disperse: we would like to take care of that. But also our kith, our extended tribe members, current, future and pending: if we take this wolf to the pack will it be able to hunt as well as the rest of us? Will it slow down the pack during migrations?  Will it dominate the herd in a year? Will it steal all our females and eat all of our cubs? Will it not pull its weight during hunting expeditions?

SunshineHaidaWolf_Blue_400x400

Credit: WickedSunshine.com

Welcome to the loopy and lupine world of metrics.

The wolfpacks of academia (read: departments) have a whole culture of ranking and assessments. Before the tenure-track wolf is accepted, a long list of future metrics are being brought out: in which packs did he PhD and postdoc? What do the pack leaders say about him? (reference letters) How good are his hunting skills (papers, conferences, invited talks) How good are his social skills? (Interview, more reference letters, phone calls).

After Dr. Wolf is finally accepted in the pack (from about 150 howling to get in), the hunting and fighting skills are put to careful periodic testing: how many grants? How much money? From which agencies? How many conference talks? How many invited talks? How are the teaching evaluations? And of course: how is the research?  How many papers? Where? What is the impact factor of the journals in which Dr. Wolf publishes? In some (I would like to think more enlightened) packs, other article-level metrics are being used. At the same time there are, of course,  the personal metrics:  What is Wolf’s h-index? g-index? h-b index?

Dear wolves, cubs and assorted members of Kingdom Animalia: what is your favorite Canis lupus related metric if at all? Poll on the right, you know the drill.

PLoS Currents: Influenza. Because knowledge should travel faster than epidemics

August 21st, 2009 No comments

ResearchBlogging.org

(Full disclosure before I start: I am an academic editor in PLoS ONE. I have no financial stake in PLoS, and as far as I know, they have none in me. They’d better not, if they know what’s good for them).

PLoS have come up with yet another cool mechanism for scientific communication: PLoS Currents. The emphasis in PloS Currents is on rapid science communication, but without sacrificing scientific rigor. To wit:

The submissions are not peer reviewed in depth, but are screened by a group of leading researchers in the field (“moderators”). The moderators will make a rapid determination as to whether a contribution is intelligible, relevant, ethical and scientifically credible, but will otherwise not impose restrictions on the nature, format or content of the contributions. Those submissions deemed appropriate are posted immediately at PLoS Currents: Influenza and publicly archived at the National Center for Biotechnology Information (NCBI).

So here we have all chief elements of scientific communication: credibility (by the moderators), timeliness (immediate online publishing) and attribution (by public archiving).  PLoS Currents: Influenza orPC:I is heavily skewed towards timeliness. The rationale being that in Influenza research and monitoring, time is of essence. After all, a report going through the usual peer review mill can take months: which is exactly the time required for a full-blown pandemic.

Not that other scientific fields are not in need of timeliness. Physicists and mathematicians have known that for almost two decades now. Nature Precedings are also providing an outlet for rapid communication in life sciences. But the combination of speed, accessibility and credibility offered by PC:I is indeed something new and welcome.

As for content: one interesting hypothesis published in PC:I is that humidity and high temperatures block aerosol transmission of Influenza, whereas colder, dryer climes facilitate it.  On the other hand, contact transmission is not affected by This would help explain the predominant winter transmission in temperate zones, vs. the ongoing yet intermittent transmission in tropical zones.  Anice Lowen and Peter Palese have communicated this hypothesis. Or rather a hypothesis. For life scientists are embedded in a culture where they are stilll used to having  only “closed stories” communicated publicly in writing. So this is quite a change. PC:I will hopefully start a trend that will help accelerate science publishing.

One final word: the technology behind PC:I is Google knol, of which I know very little about, but is seems everybody else does.


Anice Lowen, & Peter Palese (2009). Transmission of influenza virus in temperate zones is predominantly by aerosol, in the tropics by contact PloS Currents: Influenza