Why boycott Elsevier?

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, Cell.  Cell 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?

If I understand it, can I build it?

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?

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 whitehouse.gov account to vote.  It takes literally 30 seconds to create one.

Jurassic songs of lust

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.

The Ant Pompeii

Angela DePace sent me this cool video (via Boing-Boing) showing an ant colony being filled with concrete, then excavated.   Watch and be fascinated… and feel sad for the ants…

Repost: What are graduate school interviews like?

Lots of people found this post from Jue Wang useful last year, so here it is again.  Comments welcome!

Jue Wang writes:

To help 2011 graduate school interviewees, I collected some advice from current Systems Biology graduate students.  Here are their thoughts:

“Relax, have fun, don’t try too hard to impress people, and don’t get drunk at Marc’s house!” [Marc is our Chair of Department]

“Feel free to interrupt a professor’s monologue with questions. Dress warmly. Don’t be scared if your first interviewer makes you perform calculations on the fly :p”

“Have a good ‘elevator pitch’ for any research you’ve done, so you can explain it clearly and quickly when asked. You won’t be asked to recall your entire thesis, coursework, etc.”

“Don’t get thrown off if it seems like the interviewer is quizzing you. They just want to see you talk through some science with them, and don’t expect you to know all the answers. Just be honest about what you don’t know, and they’ll probably help you along.”

Update: another tidbit someone sent me today: “You should interpret the interview invitation as ‘We love you on paper, we’d like to know whether we like you in person. Hey, we hope you like us, too!'”

To give the recruits a little context to these remarks, I’ll just add a basic description of the interview weekend as my murky, pre-grad-school memory has it: a sweet hotel room, a few hours of what seemed like shooting the breeze with faculty members, meeting lots of people who inexplicably seem really excited to talk to you, and free food and drink everywhere. Did I mention the free food and drink everywhere??

I realize some might feel a little nervous about the process, especially if you take the “interview” part to mean something akin to the med school or Wall-Street job interview process. In reality it’s much more laid back. I was fortunate/foolish enough not to have given this much thought, but my first interview was with a faculty who was much taller than I realized, and somehow I found this very intimidating. It didn’t help my nerves that someone told me he was in the middle of writing a grant proposal and hadn’t slept for 3 days, and he was slightly late so I had a good 10 minutes to just sit there and hope that if I said something stupid he’d be too tired to notice. As it turns out, neither my nervousness nor any evidence of his sleep deprivation lasted more than 2 minutes into the conversation, and we had a fascinating, sprawling discussion of his research and the things we were both interested in (with a slight bias toward the former). This is basically how most interviews go.

Some of my classmates had interviews in which they were asked specific scientific questions. This can be nerve-wracking, as at least a few of the G1’s can attest, but like my classmates mention above, it’s best to just take it in stride and talk through your answers. I’ve been told to avoid trying to seem like I know something I don’t, which is confusing advice because I can’t imagine many recruits who’d be consciously trying to mislead people in their interviews. My guess is that it can seem this way if you are not engaged in a conversation and just nod like a zombie, or if you gratuitously mention ideas and jargon out of fear. Another reason to sleep well the night before and have some kind of ‘elevator pitch’ for your past and future interests, so that you can speak plainly and concisely—and therefore seem genuinely interested—about science.

One other thing I remember is being impressed and therefore slightly intimidated by the other recruits. Maybe it’s a function of how diverse — and accomplished — Harvard SysBio’s recruitment base is, but it seemed like everyone was a star at something. Also, some recruits probably went to school in the area or even worked in the department during undergrad, so they sound like they’re already in grad school. These things are a net win though, because you end up having lots of great conversations (and some insider knowledge on the best places to get pizza and whatnot).

Finally I’ll reiterate the most important advice, at least for Boston, which is to dress warmly — the East coast is very cold in late January, and the weather is more unforgiving than any of your interviewers will be. Fortunately there will be plenty of chances to warm up with beer, food, and new friends during the whole experience, so enjoy it!

Summer School at Oxford University

The Department of Statistics at Oxford University is advertising a Summer School in Genome Analysis.  Here’s some information:

Each year the Genome Analysis Group runs a project-based summer school in computational biology and bioinformatics. The next summer school will take place from 9th of July until 17th of August 2012. Applications are invited from outstanding students who will have completed at least two years of undergraduate study by summer 2012, with a strong background in mathematics, statistics, computer science, physics or chemistry.

Students work in teams of three for the six-week period on  a  cutting-edge  research  project  in  bioinformatics  and computational biology, working with leading researchers from Oxford and collaborators visiting from overseas. There is also a programme of lectures and tutorials desgined to introduce key concepts in computational biology, and to showcase recent research in the field.

Goals of the summer school

The main aims of the summer school are:

• to give students a chance to experience working on highly relevant problems at the forefront of computational biology and bioinformatics
• to make significant progress on these problems, with a view towards publishing the results
• to encourage applications for graduate programmes in computational biology and related subjects

Since three summer students, one graduate student and one postdoc work for at least six weeks on each project, there is a high chance of making real progress.

Eligibility and funding

Applications are invited from all students (UK and international) who will have completed at least two years of undergraduate study by summer 2012. No previous research experience is necessary, although students with relevant experience are especially encouraged to apply. Most previous applicants have been undergraduate or masters students, but postgraduate students and recent graduates are also invited to apply.

Accepted students will be offered university accommodation for the duration of the programme, and will receive a stipend towards living expenses.

Applications

Applications will be assessed in two rounds. Applications received by the first deadline (27th January) will be submitted for individual named funding awards.

The final application deadline is 5th March, 2012. To apply, complete the online application form.

Any queries should be directed to Ms Madeline Mitchell.

What I read on my winter vacation

It’s been a while since I posted anything serious — I can’t help but feel that I should apologize, although I’m sure that very few of you sit by your computers waiting breathlessly for the next update. Anyway, my excuse, if I need one, is that much of my spare time has been taken up with graduate program applications. And I thought some of you, especially potential future graduate school applicants, might be interested in a few thoughts I have about what goes into an application, and how it’s read (or at least, how I read it).

There are  four main pieces of information in an application for an American graduate program in biological sciences: GREs, college grades (supplemented by an academic transcript), the personal statement and the letters of recommendation. From my perspective the GREs and grades essentially act as thresholds. If your GREs and grades are above a certain level, I don’t much care how good they are. Academic achievement has some correlation with likely success as an independent scientist, but the correlation is not a straightforward or linear one. So, if your GREs are below a certain level (and you’re a native English speaker), it may raise a suspicion in me that your brain is not especially agile, and I may start looking for other evidence to support this hypothesis in the rest of the package; if your grades are poor, especially in subjects that are very relevant to your proposed area of study (or, especially at a school with rampant grade inflation), I may worry about your ability to assimilate facts and reasoning strategies; but I’m probably not going to draw much of a distinction between very good grades and perfect grades. And if one of your letter-writers explains that your very-good-but-less-than-perfect grades are due to spending too much time in the lab, I may even like you better than I would have if you had a 4.0 GPA.

After the GRE/GPA threshold is passed, I have two pieces of information left: your statement and the letters written on your behalf by people who know something about your abilities. I don’t have much to say about the statement — it should be personal, after all — except this: don’t feel that you have to treat it as an exercise in creative writing. I suspect that there’s a book out there, or more likely a website, that encourages applicants to begin their statements with an eloquently written personal anecdote that conveys their love of and excitement about science. I suspect this because so many of the statements I read start with something along these lines: “Staring into the dusky red depths of the Grand Canyon, I had a vision of someday creating cybernetic wings that would allow human-powered flight. My passionate dedication to a life in science dates from that day.”

If you really did have some kind of emotional revelation when you were 10 years old, fine. I don’t mind if you tell me about it, though please try not to be too dramatic. (I’m English, after all.) But from the perspective of a specialized interdisciplinary program, I’m much more interested in your mature thoughts about why you want to focus on systems biology in particular. It’s not an easy path, and I want to know you’ve thought about it. It’s fine to try and paint a picture of who you are as a person, but the more you can explain why you’re interested in working in this field in particular, with concrete reasons from lab or theory work you have done or courses you have taken, the better.  What you say will give me some sense of how much you know about what you’re getting into, as well as whether you can write a clear English sentence and put two ideas together in a logical order.

What about the letters? IMHO these are the most important part of the package, and what’s hard about that is that the quality of the letter is almost completely out of the applicant’s control. What I look for in letters is the following: evidence that the applicant has taken the initiative to seek out interesting research experiences, and an opinion from the person writing the letter about whether the applicant has the qualities needed to make a go of independent research. Unfortunately, what I often get is a letter that says that the applicant got very good grades in class, which I already know from the transcript. Letters of this kind aren’t helpful; nor are the letters from your swimming coach or saxophone teacher, or the personal friend who’s known you since childhood. These people may all have theoretically useful things to say about your strength of character or your work ethic, but they’re not scientists and I don’t know what “hard-working” means to them. The ideal application package has at least two letters from people who know what it takes to be a good scientist, who can talk about a substantial project that you did in their group. These letters ideally go into significant detail about how well you performed in the context of a real research environment — for most of the faculty on the committee, nothing speaks louder than a statement from an advisor about the research you personally did while working with him or her.

Have a cellular Christmas

Markus Covert pointed this one out — from the Nikon Small World competition:

Collage of single-cell confocal images by Donna Stolz, University of Pittsburg

Molecular biology carnival #6

is up at Rule of 6ix.  This carnival went through a rough patch a while back but now appears to be going from strength to strength, celebrating blogging on molecular biology topics across the web.  It’s a great idea.  Check it out.