Wednesday, August 28, 2013

Online access to papers + university libraries - info wanted

Now that we live in the Information Age, where I am reliably told that Information Wants to be Free, I'm confused by a trend that is coming in terms of how university researchers access electronic versions of journals.  (For those of you under 30, there was once a time when journal articles were published in an arcane format that predates pdf called "paper".)   The electronic availability of journals, including historical archives, has largely been an enormous boon to scientific progress.  It is far easier and faster now than ever before to do proper literature research when writing a paper or a proposal.  If I'm using google scholar or Web of Knowledge or Scopus or any other reference crawling aid, I can now find and (and if my institution subscribes or the content is available free) download copies of relevant references very quickly and efficiently.  If anything, the technology to provide this content is continually becoming cheaper and faster, since providing print content has far lower bandwidth requirements than the streaming video demands that are really driving innovation.

That is why I am concerned and confused by a trend popping up in the perpetually-financially-stressed university libraries around the country (and the world, presumably).  We all know that commercial publishers have been cranking up prices and applying annoying/evil tactics like bundling one high impact title with a dozen expensive, low-impact journals in forced package deals.  (Wiley, Elsevier, Taylor and Francis, that's you.)  Now, though, there is this idea being pushed that it would somehow be cheaper for university libraries to actually drop their subscriptions (!!) and instead use Get It Now, a product of the Copyright Clearance Center (those people you have to contact if you want permission to use a figure in a review article).  The problem is, Get It Now is misnamed; really it's Get It In Seven Minutes.  Needless to say, if you are trying to trace references and write a paper or proposal, having to wait seven minutes for every article you want to examine (which could easily number in the dozens while proposal writing) would be a major mess.   

Given that the publishers have the capability to provide content essentially instantly, and that the infrastructure to support that capability is steadily getting cheaper, and that the publishers could quite readily track download statistics (and could charge per download if they really wanted to), I don't understand how Get It Now is a positive step.  Surely if per-article billing was an economically viable approach, the publishers would do it themselves, right?  The publishes are going to recoup their costs somehow, passing them along to CCC, and CCC will pass those along to the universities, so it's hard for me to see how interposing a middleman like CCC can really do anything except slow down researchers and make money for CCC.  This idea seems to go directly against the trend of open access, public archives, etc. 

Do any of my readers work at institutions that use this service?   How does it work for you?  Is it as annoying as it sounds?  Does it actually enable your university to save money (that is, provide more or better content for the same actual cost) relative to the old approach?  A major challenge faced by universities in budgeting is that libraries don't sound as exciting as new buildings or major initiatives, and yet libraries and their services are essential to the scholarly mission of the institution.

Monday, August 19, 2013

How to: Write a response to referees

I think I'm going to start a periodic series of "how to" posts.  First up, how to write a decent "response to referees" document.  While this is pretty much common sense, it's not bad to think about it a bit in the abstract, rather than in the heat of the moment of having just received some kind of (perceived) searing blast of criticism.  In brief, assuming you get some collection of referee reports, at least one or two of which are not particularly positive, and you intend to revise and resubmit:
  • Read the reports, and then put them aside for a day, as your white-hot rage over the terrible injustice that has befallen you fades, and in the cold light of reflection you realize that perhaps the manuscript you'd sent in is not, in fact, the greatest non-fiction prose writing since Churchill's six volume history of the Second World War.
  • Now that you're in a less annoyed frame of mind, read through the reviews again, carefully, trying to understand (a) what the reviewers are actually saying, and (b) what the reviewers want you to do (assuming that's not "dry up and blow away").  Often the answers to (a) will reveal either that the reviewers did not properly understand the main point or some subsidiary point of the paper.  Much as we like to grumble about referees, you may have to admit that the fault could lie in your presentation.  Were your figures unclear?  Did the abstract and the intro make your main point explicit, or did you bury the lede somewhere down in the conclusions?  Remember, scientific papers are not mystery stories.  Springing the cool observation on the reader after a lot of setup risks the reader not realizing that the observation is cool.  Moreover, often the answers to (a) will reveal that the reviewer has thought of a possible concern or objection that you either didn't consider, or you did consider but dismissed without pointing it out and explaining your reasoning.  An extremely important part of the response process is figuring out what the main point of the referee is, and realizing that frequently it's worthy of consideration.
  • Regarding (b) above, write down and make a list of what you think the referees want you to do, or what you think it would take to address the points that they raise.    Then consider whether you want to or should do all of those things.  Sometimes the referees can be very demanding.  (We've all seen this.)  You have to use your judgment, and remember that referees are not generally gratuitously mean.  I'd say the default position should be to do what they want, unless what they want is really considered unreasonable by you and your coauthors.  This list, by the way, is a headstart on the eventual "list of changes" that you'll need to provide when you resubmit.
  • When you sit down to write your response, have the referee remarks right there.  In fact, it's a good idea to use copy/paste to intersperse your point-by-point responses.  That way you can be sure you didn't miss anything, and you are forced to write your response in an order that will seem logical to the referee.  
  • Always (always) thank the referees for your time.  Seriously.  You know what refereeing is like, and you'd like to be thanked, admit it.  
  • Point out that after this process you believe the paper is much improved (it will be, too, assuming the referees were really on point and not just asking you to cite their seminal work on the topic at hand), and if possible explain why.  (e.g., we believe that our main point is now much clearer)
  • Always be polite and professional.  If you fly off the handle in your response, even if the referee is overtly hostile, it won't do you any favors with other referees or the editor.  Similarly, just as tone is difficult to convey in email, I suggest avoiding attempted jokes or sarcasm.  This is a professional communication - keep it that way.
  • Try to be timely about revisions.  It's much better to get revisions done while everything is fresh in your mind, rather than letting things linger.  (Don't write them in the heat of the moment, though.)
In your accompanying cover letter when you resubmit, make sure that you emphasize the changes you made in response to the referees.  Also, it doesn't hurt to point out to the editor if you think a referee either missed the mark or seems not to be objective, but it would be best to do so in a very professional way.  Calling the referee an idiot won't win you any friends, particularly since the editor likely chose the referee.  Still, if you really think the referee made serious mistakes, or was not competent, or didn't read the paper, you should bring that to the editor's attention in a professional way.  Again, this kind of response is an important part of your repertoire of professional communications, so it's best to get in the habit of writing them well.

That's it for now.  I'm sure I've left out points - please feel free to bring them up in the comments.

Tuesday, August 13, 2013

Rankings and metrics - yet again

I (along with my departmental colleagues) was very happy to see this.  My department does extremely well in a particular ranking scheme (described in the original paper here and implemented online here, though you need to ask for password access) that asks, essentially, what fraction of the papers published by a department fall into the top 10% in terms of impact in an area.  We can debate about the flaws of any ranking scheme (hint:  they're all imperfect, because quantifying scientific quality and impact in a single number is fundamentally wrong-headed).  Still, it is nice to see an approach that agrees well with much intuition (that is, the usual top-10 suspects all look pretty good; schools that don't do much research in an area rank lower) where Rice does well. 

Saturday, August 10, 2013

A new kind of solid - why "q-glass" really is weird and interesting

As long-time readers here know, I'm not a big fan of hype and press releases.  While it is very important to let people know what academic scientists and engineers are doing, not everything needs to be trumpeted from the rooftops as a huge breakthrough or a paradigm-altering thunderbolt.  However, this new result (the actual paper is here) is genuinely weird, unexpected, and exciting (at least to me).  The authors claim to have discovered a truly new kind of solid.  Let me break down what this means and why it's surprising.

A solid is a material that resists shear deformation - if you exert a certain force horizontally across the top surface of the material, the material will deform a bit until it's internal forces balance your applied force, and then deformation will reach some constant amount.  (In contrast, a fluid will keep deforming continuously!)  The most ordinary solids people know about are either crystalline (this includes polycrystalline materials made up of many crystal grains) or glasses.  In a crystalline solid, the atoms have taken on highly symmetric spatial arrangements.  That is, the atoms aren't separated by random distances, but integer multiples of certain particular spacings; similarly, crystals are not isotropic - there are particular directions along which atoms are arranged.   In contrast, simple liquids are isotropic, and except for some typical nearest-neighbor distance set by the atomic or molecular size, there is no other spatial ordered arrangement.   When a solid crystallizes from a liquid, it is a collective phenomenon, a phase transition, and this happens on cooling when the free energy of solid phase becomes lower than that of the liquid phase.  Quasicrystals (see 2011 Nobel for Chemistry) are in these senses crystals - their symmetries are just more subtle than those of ordinary crystals.

Glasses (including those made from polymers) are different.  They resist shear, too, but they do not have the long-range, periodic/anisotropic arrangement of constituents seen in crystals.  Instead, upon cooling, glasses become solid (meaning that their viscosity diverges toward infinity) because the constituents become "kinetically hindered".  At the risk of dragging up controversy, the simple description is that there is no true glass phase in the thermodynamic sense - glasses are rigid because the constituents can't readily move out of each others' ways, not because there is some true collective thermodynamic stability (involving free energies) at work. 

The authors of this new work have found something special that they have termed a "q-glass" while looking at what happens in the solidification of a molten mixture of aluminum, iron, and silicon.  In the resulting solids, they find nodules of a new material (Al91Fe7Si2, approximately) that is definitely not crystalline or polycrystalline (no preferred lattice spacings; completely isotropic).  At the same time, the material does form out of the melt through a genuine first-order phase transition (!), and therefore appears to be highly ordered in some sense (both distinguishing it from a glass).  It will be very interesting to learn exactly what is going on here, and whether there are other materials that have these peculiar features.

Wednesday, August 07, 2013

Peer review, tone, and common courtesy

I'm back, though now I'm in the writing-six-things-before-the-term mode, so blogging will likely continue to be sparse.   Several of my friends pointed out this article in the Chronicle of Higher Education regarding the tone of correspondence in the peer review process.  In short, some fraction (from my own experience, I'd say maybe 15%) of "negative" reviews go beyond pointing out issues that need to be corrected to improve the paper and instead are genuinely hostile and nasty - basically tone and phrasing that the reviewer would very likely never have the nerve to use face to face.  Interestingly, those of us who experience the peer review process beat the rest of the world to the observation of a behavior pattern that is now realized to be common on the internet.

I wish I knew the solution to this.  Removing the blindness of the review process is one possibility, though I do worry that the same petty, vindictive people who write reviews like this will then engage in additional unprofessional behaviors toward people that they perceive as slighting them. 

The point of the review process in science is to make sure that correct, clear, original science results get disseminated in the literature.  We are all (allegedly) on the same side.  If people would just adhere to that, then reviews could be much more constructive in tone (e.g., instead of "The authors are just plain wrong", wouldn't it be better to say "I'm concerned that there are some problems with steps 1 through 4"?).

I am worried that there is a general erosion in common courtesy as well.  I know this makes me sound like a grumpy old man, but again there are some people who use electronic communications in general as an excuse for rudeness.  Taking the time to say "please" and "thank you" is never time poorly spent.