12
Jul
17

Academic Publishing

In my years as a lecturer at the California Maritime Academy (CMA)1, my activity in reading research papers slowed to a crawl.  There is no formal expectation of research for lecturers, but the more proximate cause is simply that teaching course loads are very high for lecturers, and there was scant time that could be spent on research.  Now, however, I am a new assistant professor, which means that research is expected, and I have some time to spend on doing it. The first step, after several years away from intensive research, is to re-familiarize myself with the state of the art in my research subspecialties. To do that, I need to read research papers. A lot of them. And that’s where I encountered a scourge that I had no significant prior experience with: the paywall.

I was certainly familiar with the concept, and I had encountered some while reading various publications online like the New York Times or the Wall Street Journal, but I hadn’t experienced the paywalls of academic publishing.  When I was a grad student, the University of Oregon was (and is) large enough and well-funded enough that pretty much all the journals I wanted to read were available with just a few clicks as long as I was on campus.  I could cast a wide net, sift through dozens of articles looking for information, find or not find what I was looking for, and continue onward having never left my desk or paying a penny.  It was an efficient and gloriously simple way to conduct research.

When I first started reading papers (or trying to read papers) at CMA, I knew that I wasn’t sitting within the walls of a major research institution, but I thought that I’d try doing the same thing I did at University of Oregon.  It did not go well.  A conversation with our librarians later, I learned: (1) online access for physics journals is very poor, and this is because CMA only has a few physicists, and most of those physicists have affiliations at larger schools through which they can get their access2, (2) I can read any article I like (there’s the California State University (CSU) system advantage!), but I need to order it via a sort of digital interlibrary loan, which takes between 0.5 and several days to fulfill, and (3) there are journals that are available CSU system-wide, but their number has been dwindling because the budget for them is flat, and the cost of the journals has been going up.

All this provided everything I need to know to go about my research.  Sure, it’s a pain in the ass compared to a few clicks for instant access, but I can get the papers I need.  However, the situation got me thinking about academic journal publishing.  Why can’t libraries afford more journals?  Why are journals so expensive?  What if I didn’t have an academic job, but felt like trying to read about or do some research on my own time?  Why, when most research papers are produced by researchers paid by public institutions and funded by grants from public institutions, is there a paywall at all?  My inquiring mind wanted to know.

As with most things in this world, it turned out a lot of people had been doing a lot of thinking about this issue prior to my interest in it.  After reading for a while, I’ve formed some opinions, but I’ll save those for later.  First, some facts and figures.

  • Most journals do not require a submission fee, which means that anyone can submit their manuscript. Yay! Journal editors spend some of their time culling the herd of submissions before sending out the remaining ones for peer review.
  • Most journals get most of their money from subscriber fees, and most subscribers are institutions like libraries, not individuals. This is the ‘traditional’ model of funding academic journal publishing. If you aren’t a subscriber, you can buy individual articles for something in the neighborhood of $30(!).  Publishers add value in various ways.  Reputable ones have excellent editors who filter out submissions that don’t fit the scope or pedigree of the journal and coordinate the all-important peer review process.  There are reproduction and distribution costs for journals that still have a print presence rather than online only.  Online publications must host the material, archive it, and index it so that readers can find it easily.
  • More recently, so-called ‘open-access’ journals have begun to grow in popularity. In this model, when a paper is accepted for publication, a fee is paid by the writer of the paper to publish it.  The paper is then free to read for anyone in perpetuity.  The fee is relatively large, typically $1k – $3k.
  • Lastly, the Internet exists, so there is a very low barrier to simply ‘self-publishing’ a paper on one’s own webpage or posting it on something like arXiv3. Everyone can read it, and you don’t have to pay to publish it.  However, there are issues here.  First and foremost for someone like myself is that this sort of publishing holds almost no weight when it comes to tenure and promotion. Research publications need to appear in academic journals if you want to stick around. And unfortunately, you usually can’t publish your paper on your webpage and then submit it to a traditional journal as well. Some simply discourage it, but others, particularly the ‘name’ journals, will not publish it if you also self-publish.

So, what do I think about all this? Well, I think that most journals are too expensive for the value they add.  Costs for subscriptions have gone up at about triple the rate of inflation for decades.  Journals have mostly gone online, which should reduce costs associated with reproduction, printing, and distribution. The peer review process, though coordinated by the journals’ editors4, is done by the writer’s peers (other researchers) who aren’t paid.  Copy editing is mostly done by the writer and in the peer review process, not by editors.  Even typesetting is mostly automated. The cost run-up, at least for most journals, seems entirely disproportionate.  And although the  open-access journal model is, I think, overall a better system, there is still a significant barrier to publishing, albeit now it is on the writers’ side of the equation.  Not everyone has a couple thousand dollars to get an article published.

All this doesn’t even address the following: if the reviewers aren’t paid and are often employees of public institutions, and the research that led to the paper is funded, quite often, by public dollars, how is it fair that Joe Q. Public (or me) can’t read anything but the abstract if the paper goes into a traditional journal?  Adding insult to injury, commercial, for-profit publishers’ margins are around 25%, so they are profiting handsomely while not writing the content or reviewing the content or funding the content5.

Justifiably, there are some who look at all this and want to burn it down6. Two individuals of note in this category are Aaron Swartz and Alexandra Elbakyan.  A relatively famous computer programmer, Aaron Swartz engaged in political advocacy for freedom of information, and subsequently more dramatic ‘freeing’ of public records and academic journal articles from behind paywalls.  His most dramatic stunt, using an MIT guest account to download hundreds of thousands of articles from JSTOR7, got him in significant legal trouble, and he tragically committed suicide while free on bail.  Alexandra Elbakyan started Sci-Hub in 2011, a website that provides access to millions of scientific articles that are normally locked behind a paywall.  Predictably, commercial publishers were not pleased, and one of the largest, Elsevier, filed suit against her and managed to win a judgment against her that resulted in sci-hub.org being shut down.  Also predictably, since the material is primarily hosted abroad and the internet is a big place, Sci-Hub is still up and running at other domain names.

Despite my own frustrations with the system as it stands, I don’t think that simply ignoring the law is the correct way to proceed8.  There has been progress, both in terms of publishing models and in policy.  Though open-access publishing models are currently expensive for writers, there are programs for writers with demonstrated financial difficulties, and universities or granting agencies will often pick up this publication cost.  Open-access journals represent greater than 10% of published articles, and that proportion is growing.  Many universities are adopting some flavor of open-access policy, in which their professors’ papers are published in a free repository after (typically) a year-long embargo.  On the other end, granting organizations are starting to demand the same sort of thing – the National Institutes of Health, the National Science Foundation, and the Bill and Melinda Gates Foundation (among others) – currently require that papers that relied on funding from them be open-access after a year-long embargo.  Academic libraries, the predominant subscribers to various academic journals, are pushing back more and more on journal subscription costs, motivated by flat purchasing budgets and massive run-ups in subscription costs.  In addition to all this, the publish-or-perish nature of gaining tenure for academic researchers, a major source of fuel for the articles going into all these academic journals, is being subjected to some scrutiny9.

These are all encouraging developments, but a great deal is left to be done. Researchers, no matter their financial means, should be able to read about the current state of their field.  Researchers, no matter their financial means, should be able to publish their work if it is of high quality.  This is currently not the case, and only by examining the whole picture – the article writer, the expectations of the writer’s employer, the cost structure of publishing, the motivations of the publisher, and methods by which the articles are disseminated – will meaningful progress be made.  For me, other than talking about it here, I’ll start by publishing my stuff in open-access journals.  Fingers crossed that CMA will want to pick up the publishing fee!

1 Known by many other names, which is confusing even to people who work there like me.  The most recent offical name is California State University – Maritime Academy.  Cal Maritime is another, more common usage.

2 Which doesn’t help me.  Blerg.

3 arXiv is an awesome pre-print archive (read the ‘X’ as the greek letter it resembles to get the cleverness of the name) that is free and run by Cornell.  It’s a physics and math thing for the most part, and is not a peer-reviewed journal, though a lot of eyeballs see the papers there.

4 Though even this coordination is mostly done through an automated online system for the referees.

5 There are partial exceptions to this, but not many.  Also, the editors of many journals do review the article, but not anywhere near the extent of the unpaid peer reviewers.

6

disaster-girl

7 A massive online journal article archiving and indexing service that requires a subscription to view its contents.

8 Though it’s certainly convenient until you get caught.

9 Well, at least a little.  Check out this article for instance.  I particularly enjoy this quote: “…lamenting that academic scholarship had become fixated on generating lots of pieces of knowledge — bricks — and was far less concerned with putting them together into a cohesive whole.  In time, he worried, brick making would become an end in itself.”

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11
May
17

Summer 2017

With the current state of the academic calendar at California State University – Maritime Academy, faculty who aren’t on what is commonly referred to as “cruise” have quite a long summer: from the fourth week of April to the last week in August.  The trade-off is that the semesters are a sprint.  None of the usual breaks except for the non-negotiables like Thanksgiving Day, Martin Luther King, Veterans’ Day, and, because this is California, Cesar Chavez Day.  And teaching loads are high compared to most colleges/universities.

This means that 90% of research by faculty occurs during the summer.  As I piece together what will become my research program at Cal Maritime, I’m endeavoring to catalogue my efforts (as well as a few other things) this summer.  It will help me be productive and organized, and hopefully it will make for some entertaining reading as I flail impotently in full view of the Internet.  Something for everyone, I’d say.

08
Nov
14

Talking Cars

Tom Magliozzi of the National Public Radio (NPR) program Car Talk died on November 3rd, 2014 due to complications from Alzheimer’s disease. He was 77 years old.
I’ll admit that when I heard this news on the radio, I started crying. Those of you who know me also know that I cry at a lot of things: the big, life-changing things and quite a few little things. Nemo’s clownfish mom (spoiler alert!) dying in the first ten minutes of Finding Nemo? I cry. About every other StoryCorps segment on NPR? I cry. So – I have this tendency.
Still, I don’t typically break down blubbering when the famous die. For instance, though the death of Robin Williams was a terrible tragedy, my eyes did not immediately start leaking in response to that news1. And yet, there I was, rolling into the parking lot at work on Tuesday morning with tears streaming down my cheeks. Others have done the job of eulogizing Tom better than I can2, but the guy was a feature in my life for as long as I can remember, so I feel obligated to say, well, something.
I don’t really know when my parents started listening to Car Talk, but I was young. Young enough that I don’t even distinctly remember how I reacted to the program other than a vague sense that I liked it, and that it was on most Saturdays. It’s not as if the whole family would gather around the radio and sit rapt as Car Talk “wasted” one of our perfectly good hours, but it was/is a constant presence in my memories of weekends growing up. I remember my Dad always doing this ridiculous little dance to Car Talk’s bluegrass intro music3. I remember someone, maybe my Mom, commenting that perhaps Tom and Ray shouldn’t laugh at their own jokes so much. This admonishment made me try to stop laughing at my own jokes, though I don’t think it stuck. I remember going away to college and occasionally flipping on this little clock radio my parents got me on Saturday mornings to listen to Car Talk – then realizing it made me a little homesick. I remember going away to grad school and listening to Car Talk almost every weekend. At that point, it had become something that centered me a bit and reminded me where I had come from and what I was doing there in Oregon. Some small part of my mild success during my first year of grad school should be attributed to the Magliozzi brothers.
More recently, my Car Talk listenings had become more sporadic. Maybe I was finally settling into my own identity, finally re-defining my home as wherever my wife and I were rather than back in Chippewa Township4. Whatever it was, I was catching my Car Talk fix going to and/or coming back from the Berkeley Bowl. I’d catch a horse eating someone’s steering wheel on the way in, and if I was lucky, a Katherine with a K5 telling Tom and Ray about the whizzzzz—-wub—–wub—wub–wub-wub-wubwubwubwubwubwubwub sound her car was making when going around a lefthand turn that was greater than 90 degrees, oh, but only during the winter months. And on odd-numbered days. And only on even-numbered days if it had snowed the previous day. Stump those chumps, Katherine, stump them good.
And now, well, here we are with the Magliozzi brothers down to half strength and retired to boot. Mr. Berman, the often-good-naturedly-maligned executive producer of Car Talk has stated that there are enough unique Car Talk segments to fill eight years of re-runs. I sincerely hope that he is incorrect, and that the edited re-runs we now hear continue to be run for many years beyond that. After all, my wife and I are expectant parents of a daughter that I hope will have her sense of home and humor partly defined by the voices, laughs, and intellects of the Magliozzi brothers. Thanks to both for many years of entertainment, knowledge, and memories.

1 And to be clear, I’m a big Robin Williams fan. Even went to see Patch Adams, though I’d like that time back please.
2 Try these for good stuff from people who knew Tom personally:  NPR story, Car Talk memorial
3 If you’re interested, the piece is called ‘Dawggy Mountain Breakdown’ by the David Grisman Quintet. Oh, and thanks Dad, I have inherited your dance moves.
4 Yeah, that sounds like pop-psych crap to me too, but hey. Oh, and Chippewa 4 life playas! FOR LIFE! I’ll always love Oakville Road.
5 Obviously.

18
Jun
14

Knees, Rabbits, and Super Rabbits

The thread of a conversation:
First, my lovely wife and I were lying on the couch after watching an episode of Star Trek: The Next Generation1, when I commented that her knees were kind of small. She claimed that her knees were normal and in fact that it was my knees which were unusually large and weird. We agreed to disagree. She then started wondering how it was that knee replacements are done2. Are all the ligaments and tendons cut and re-attached?  I suggested that perhaps they were moved out of the way and that only the ones attached the joint itself were removed.  She replied that if the joint was titanium, then biological tissue could bond to it and vice versa.  She revealed that she had learned this while reading The Disappearing Spoon: And Other True Tales of Madness, Love, and the History of the World from the Periodic Table of the Elements, which describes the original experiment involving a rabbit and a very thin piece of titanium being placed over its healing leg bone so that the process of how bone marrow produces new blood cells could be observed but not be exposed to the environment.  Creepy.  The scientist3 found that the titanium was bonded to the bone as the bone itself healed.  My wife expressed sadness that a rabbit had been subjected to such a trial.  I agreed, though I suggested that the rabbit had likely been further experimented on to determine the extent of titanium’s ability to bond to bone until the skeletal structure of the rabbit was mostly made up of titanium. Horrifying as this must have been at the time for the rabbit, it now had super powers like Wolverine4, and once it had escaped, it could use its powers both for good and to visit a righteous vengeance upon its oppressors and bunny oppressors everywhere. Soon, as its skills developed, all the warning its enemies would receive was a slight rustling in the brush, and then a brief silence as the rabbit launched itself5 through the air toward the jugular of its foe.  Later in its evolution, I concluded, the intensive training and its unique bone structure would allow it to achieve sub-orbital flight with a single hop.  The only warning its enemies would then have was the sonic boom the bionic rabbit would create as it re-entered the troposphere6.  Unfortunately for them, this forewarning would be unlikely to save their lives.  One hop later, and the only evidence that the bionic bunny would leave behind was the resulting carnage and a few errant hare hairs.
“It needs a name”, my wife said.  “Ellie Junior”, I responded.  “Not very superhero-like”, she responded.  I promised to come up with something more appropriate if something of this sort ever came to pass.
And then I went off to brush my teeth.

 

1 Eye of the Beholder, Season 7.  A good one.
2 My father recently had one of these, so this wasn’t completely at random.
3 Dr. Per-Ingvar Branemark.
4 Snikt, snikt.
5 Hop!
6 Note: the bunny would require specially-made goggles.

15
May
14

Doodling

I think everyone doodles at some point.  Probably during a meeting that should have been over a half hour ago.  Anyway, I doodle, and if I’ve figured out the tool for adding an image to a post, you’ll be seeing an example in the space below.  For a more talented doodler whose style I approve of, go here.

Tricolor!

Tricolor!

17
Aug
13

Hey Abbott

About eight months ago, I promised readers of this blog a post on beer.  My strict publication schedule has finally brought us to that post in a timely manner.  Rather than write on beer at-large, I have decided to approach things a beer at a time – and then elaborate too much in the usual fashion.

Earlier this week I imbibed a brew from the Ommegang Brewery1 of Cooperstown, New York.  They call it “Abbey Ale”, and it is styled after the Dubbel ales produced by those wizards of beercraft, the Trappist monks of Belgium. Here is some information that greets the viewer of this 750mL, $9.99, corked bottle of beer:  8.2% ABV, a silhouette of two monk-like creatures clinking their goblets together, and the following script, “Ale Brewed with Licorice Root, Star Anise, Sweet Orange Peel, Coriander, and Cumin”, followed by, “Rich, Fruity and Aromatic Burgundian Brew”. All very nice, though it is this label information that has made this beer the second (maybe third) Ommegang brew that I’ve tried. Cumin, weird. Coriander, weird. And I dislike licorice. I also wasn’t sure what “Burgundian” really meant in relation to a beer, and I’m still not sure2.

Still, their Three Philosophers ale was ever-so-tasty, so I trusted the brewer if not this particular brew3.  So, I bought it, brought it home, carefully considered it, removed the cork, and poured half a glass in such a manner as to not disturb the settled yeast carcasses over much, yet produce a healthy ‘head’ of bubbles on the poured glass.  I read somewhere that this last bit (the pour) is crucial.  CRUCIAL.  Hard to say if I accomplished the first goal of the pour, though I can attest to achieving the second part.  Anyway, my impressions of this fancy brew once I had a sniff and a taste were – mixed.  All the visual cues were pleasing.  Nice carbonation and attractive color, a warm brown with a touch of red.  The problems started as soon as I lifted the glass toward my face.  The aroma of the beer had a fair amount of that anise/coriander in it, at least to my nose, and this is not what I’ve been conditioned to expect in smelling a beer.  Persevering, I took a drink, and was greeted by much the same.  All the herbs, so proudly displayed in the label text, were equally proudly displayed in the taste and odor of the brew.  This is not to say that the herbs completely dominated the beer.  I’ve had beer, fruity beer usually, in which that occurs, and it is akin to an assault.  No, here it is more akin to a slightly-too-firm handshake.  Not unpleasant, but perhaps a little uncomfortable.

Now this bottle cost me about eleven dollars, so I’m clearly not a particularly frugal person, but I’m also not such a spendthrift that I would let the rest of the bottle go to waste just because I didn’t like the first sip.  Luckily, because the herbs, though assertive, are not overpowering, the beer improves with continued imbibing.  You might ask, doesn’t every beer do this?  The short answer is yes of course4, but the point I’m trying to make here is that the unusual flavors of this beer grew on me.  By the time I was half a glass into the bottle, the taste and aroma of the beer became familiar, less obtrusive.  When I encounter a beer that is a little off-putting to start, it is not common that by the end of the bottle I end up rather liking it.  I think that if I had (1) a more open mind about how beer was meant to taste and smell, and (2) liked anise/licorice, I might have enjoyed this beer thoroughly from start to finish.  As it is, however, I don’t think I’ll be buying it again.  At least not at that price.

1 Also the brewers of a licensed promotional beer for Game of Thrones called the Iron Throne Golden Ale.  A quote from the brewer, “With a Lannister currently on the Throne, it made sense to do a delicate, but piercing Golden Blonde Ale with Noble hops.”  Well spoken, sir.
2 The only thing I could come up with after a bit of looking around is that good Burgundy wines are almost always hailed for having very complex and rich flavors.  I believe this is the quality that Ommegang meant to attribute to this beer.  Still, it is so unclear to the reader that I can only assume that the brewer was just attempting to piggyback on the good name of the Burgundy wine region, despite this brew having nothing to do with it.  Very odd.
3 Made this mistake with Dogfish Head Brewery once at the Oregon Brewers Festival.  The brewers of the very fine 90 Minute IPA also make the Black & Red.  Stay far, far away from that one my friends.  Syrupy, heavy, very fruity, high alcohol, and very, very minty in the middle of the hot Oregon summer.  Mint?  What?
4 Well, to a point anyway.

02
Aug
13

Header Mark II

You, a reader of my blog, are now enjoying new and improved(?) scenery at the top of the page courtesy of my recent trip to Acadia National Park. Pictured is what I believe to be minuartia groenlandica, or the mountain sandwort.  Translated further, it is a plant (wort) that lives in alpine to sub-alpine environments amongst granite ledges and the gravel that results from those ledges’ erosion.  Aptly named and described by its wiki, I think, since this is exactly the kind of place I found it. It is relatively rare in Maine because the state is on the southern end of the flower’s range and the environment that it likes isn’t found in too many places there.  The Maine Department of Agriculture, Conservation, and Forestry (more specifically the Bureau of Geology, Natural Areas, and Coastal Resources within the aforementioned Department1) says that it hasn’t had a documented observation of one of these since 2002.  This suggests to me that either they haven’t bothered looking, or 2002 is when the particular webpage I am looking at was written.  Maybe both of these things are the case.

Anyway, I found all this out by searching the Internet, which is fantastic. I know that statement kind of makes me sound elderly, but I think anyone with half a measure of curiosity should be able to take a step back and wonder at the combination of clever technologies that allows me to start with a digital picture, type “tiny white flower Pemetic Acadia National Park” into Google, find a picture of the same flower captioned “mountain sandwort” on the hikenewengland.com webpage, type “mountain sandwort Acadia” into Google to get to a pdf describing “Focus Areas of Statewide Ecological Significance: Acadia East and West”, which gives me the scientific name of the flower, etc, etc.  Real life is science fiction.  Sort of.  I suppose I won’t be truly mesmerized until I can snap a picture of something relatively obscure like this flower, have my camera wirelessly transmit that picture to a server on the internet, which will run a sophisticated image analysis algorithm on it to identify the flower, compile the sum total of human knowledge on that flower, attach a few other pictures of the same species and related species for reference, and zip all that back to me in, say, a quarter of a second.  You can actually do this with Google Goggles, but it works only a very small subset of the world so far.  Until they get their act together2, I will have to find other things to marvel at.  Shouldn’t be too difficult.

1 Bureaucracy, what bureaucracy?
2 I mean, come on, right? Clearly, they are just twiddling their thumbs down there in Silicon Valley.