Computational modeling of signaling course at NIH

March 1, 2012 § Leave a comment

In June, the Laboratory of Systems Biology at the National Institute of Allergy and Infectious Diseases (NIAID, NIH) will offer a short course on computational modeling of cellular signaling processes using the Simmune modeling tool set (June 4-8).

The first part of the course will provide a hands-on introduction that is tailored towards biologists without prior experience in modeling but with an active interest in quantitative and spatial aspects of cellular behavior. The second part of the course will introduce computational modelers with a solid programming background to the possibilities and techniques for using the programming libraries of Simmune in their own projects.

Travel and lodging scholarships are available.  Further information here.

Research Works Act withdrawn

February 29, 2012 § 2 Comments

This is good news: the Research Works Act, which sought to prevent the government from requiring that work that they fund should be made publicly available, has been withdrawn. Elsevier withdrew their support for the act a couple of days ago.

Some are interpreting this as a change of heart on Elsevier’s part.  Mmmm.  I guess that’s within the bounds of possibility.  Or is this a case of “he who fights and runs away lives to fight another day?”.  Note this sentence in Elsevier’s press release: “While we continue to oppose government mandates in this area, Elsevier is withdrawing support for the Research Work Act itself.”


Pay it forward

February 25, 2012 § Leave a comment

Andrew Murray on why teaching is important.  One of his reasons: someone taught you, and you should pay them back by teaching someone else.  Watch the video to learn the rest.

Why boycott Elsevier?

February 23, 2012 § 16 Comments

Lots of people have suggested that I write something about the recent effort to boycott Elsevier.  I don’t usually like to write about the politics of science, mostly because I usually don’t have much to say that hasn’t already been said.  For this particular bit of science politics, though, the problem may be that I have too much to say.  I’ve been in and out of science publishing for much of my working life.  I worked for a company that was acquired by Elsevier, and left the company (and publishing) as an indirect consequence of the acquisition. Two of the journals I put blood, sweat and (occasionally) tears into getting started are now published by Elsevier.  I have friends who still work for Elsevier.  I have friends who left Elsevier-acquired journals for Open Access journals.  Nothing I might say can be considered unbiased.  At the same time, perhaps I know a bit more about the topic than some of the other people writing about it.  Or at least I know different things.  So be warned: this may be a long one.

For those who haven’t heard about the Boycott Elsevier movement, it started when the Fields medalist Timothy Gowers announced a policy of non-violent non-cooperation with Elsevier.  Triggered, I think, by Elsevier’s support of the Research Works Act, which as I have mentioned before aims to prevent the US government from encouraging or requiring open access to government-funded research, he decided to publicly announce that he would not publish in Elsevier journals, nor would he serve on editorial boards or as a reviewer for them.  In singling out Elsevier for this treatment, he pointed out that Elsevier is especially rapacious in the matter of charging for their journals, and uses a sharp business practice called “bundling” (forcing libraries to buy bundles of journals in order to get the most popular journals) to maximize the subscription fees they receive.  Because Elsevier, through luck or good judgment or shrewd acquisition, has quite a number of popular journals in its stable it can bully libraries in this way quite effectively.  It is a very profitable company; in 2010 it had revenues of $3.2 billion, of which 36% was profit.  That puts Elsevier way ahead of the average publishing company, which (in 2008) made an average return of 7.9%.

Gowers points out that it’s not useful to characterize Elsevier’s actions as immoral: they are a large company, they have shareholders, and in a capitalist world there is nothing unusually evil about doing your legal best to maximize your profits and protect your interests, including lobbying Congress to pass laws that work in your favor.  But he is personally offended by Elsevier’s abuse of power, however legal and corporately appropriate it may be, and so he is, in essence, withdrawing his labor.  At the time of writing, over 6700 people have promised to do the same. 1275 of these signatories identify themselves as mathematicians, and 994 as biologists.

Of course it’s absolutely reasonable and right to withdraw your support from any enterprise that morally offends you.  I take my virtual hat off to Dr. Gowers and his fellow travellers.  Considered as an effort to damage Elsevier and thus change the world of scientific publishing, though, this movement brings to mind a couple of questions.  The first is, when is it OK for a publisher to make money on publishing scientific journals, and when profit is OK how much profit is reasonable?  The second is, does this effort have a chance of working?  Neither of these questions has a simple answer, to my mind.  It may be best to take the second first.  So, how many scientists need to work to rule for Elsevier to be hurt?

Elsevier publishes journals in all areas of science, and the answer is probably different for each individual field.  In biology, one question is how much community shunning it would take to hurt Elsevier’s top journal, CellCell is generally felt to be one of the top three journals in biology (known variously as “the glamor mags”, SNC (for Science, Nature, Cell) or “the rejectionist journals”).  I’ve never worked for Cell, though some of my friends have, but I did work for Nature once upon a long-ago time.  At the time, Nature was receiving about 120 biology manuscripts a week.  My guess is that probably ~30-40 of these papers could have been published in Nature without raising any eyebrows, but because of a strict page budget set by the publisher we were only able to accept about 12 of them, or about 1 in 3. Cell‘s numbers probably aren’t too different, suggesting that even if ~1/2 the scientific community decided not to publish in Elsevier journals, Cell would still be happily able to fill its pages.  There would eventually be an effect on quality, but it would take more effort than you think to get to a point where it’s noticeable.

Another question is how much it would take to damage one of Elsevier’s less dominant publications, of which there are hundreds.  In mathematics, the community decided that the journal Topology was ridiculously overpriced, and the editorial board for the journal resigned en masse — an apparently fatal blow.  Could an effort like this be effective for biology journals?

Perhaps.  We need to remember that mathematical journals in general are far less powerful than biological journals. The mathematics community is much smaller, and it’s easier to know for sure who contributed what and how important the contribution was.  A preprint on arXiv is just as visible as a paper in a journal (if not more so).  The mathematics community decided it could do without Topology, and was able to take coherent action to get rid of it and move on.  It wouldn’t surprise me at all if there were Elsevier biology journals that the biology community could do without, but it seems to me that the current boycott effort is too diffuse to be likely to be successful.

If one wishes to send a message to Elsevier that many of their journals are overpriced, perhaps the most successful strategy would be to attempt to copy what happened to Topology for a selected few journals (~10) for which there seems to be little justification.  For example, one might choose journals that compete with a perfectly good society journal or open access publication, or both, and that are noticeably overpriced given the quality of the journal.  The goal would be to persuade the entire editorial board to resign and spread the word throughout the biological community that nobody should sign up to replace them, and nobody should submit or review papers.  If enough of the community agrees that these specific journals are unnecessary and overpriced, there might then be a real chance of killing them.  (If not, a new editorial board will sign right up, and many people won’t even notice the change.  In a community as large as the biological community, with commensurately diverse opinions, this seems to me to be a real danger.)

I think a strategy like this might have some chance of success, and of delivering a message that will be heard.  My guess is that the current boycott — even though it’s generating lots of buzz, and articles in the NYT, and opinion pieces in the Boston Globe comparing it, bizarrely, to the Arab Spring — has little chance of making any difference to Elsevier in biology, though the situation could be very different in mathematics.  A targeted approach doesn’t sound as grand as boycotting the whole of Elsevier, and has the further disadvantage that it requires consultation and agreement about which journals are most egregious before anything can be done. But if it works, then one could go on to the next 10 most unnecessary and overpriced journals, until the only journals that are published are those whose prices don’t generate too much outrage.

Which leads me back to the first question: when is it OK for publishers to make a profit on a journal, and how much profit is it OK for them to make?  What (if anything) does the community want from publishers, and how much are we willing to pay for it?

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If I understand it, can I build it?

February 16, 2012 § Leave a comment

It depends on your definition of “understand”… and possibly your definition of “build”.  Thanks to Pam Silver, I’ve belatedly become aware of the CAGEN competition.  CAGEN, which somehow trips off the tongue less elegantly than iGEM (but perhaps I’m just not used to it yet) stands for Critical Assessment of Genetically Engineered Networks, and the competition sets challenges for the synthetic biology community that “if achieved, would imply that significant improvements in the state of the art have been made”.  This year, the challenge is to design a circuit that provides a robust gene response: rapid expression of a fluorescent protein at a controlled level (moving rapidly from 1x to 10x) upon the introduction of a chemical inducer, with minimal variation in expression between cells.  It should work both in E. coli and S. cerevisiae, be sustained over time, and have minimal temperature-dependent variation.  Specifics, including the metrics to be used, are on the Challenge page.

Think you have a design that will work?  You have until June 15 to submit it.

Are you in favor of open access publication?

February 14, 2012 § Leave a comment

Then sign the petition to oppose the Research Works Act. Do it now, or the petition will fail. Spread the word.

Most of you know that Congress passed a bill in 2008 requiring that papers resulting from NIH-funded research to be deposited in PubMed Central no later than 12 months after publication.  This new Act reverses that bill, and furthermore forbids ANY effort by any government agency to make research more accessible illegal.  Mike Eisen has a detailed explanation here.

Number of votes required (by Feb 22!) for the petition to matter: 25000.  Number of votes at the time of writing (including mine): 1395.

Let’s kick it up a notch, folks.  Please, do not be deterred by the fact that you need a account to vote.  It takes literally 30 seconds to create one.

Jurassic songs of lust

February 7, 2012 § Leave a comment

This is cool: a paper in PNAS describes the reconstruction of the chirp of a Jurassic cricket, based on the anatomy of the forewings in fossils, plus a phylogenetic comparison with modern crickets. A song from ~165 million years ago. Hear it here.

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