28 August 2006

Abbrev. commod.

I've spent the last three of four days making revisions to my most recent manuscript, which is getting shipped overnight to the editorial office today. Yay! In doing so, however, I spent a lot of time thinking, "There must be an easier way."

First, this journal has incredibly stringent guidelines for digital art. The guidelines for their artwork are on the authors' instructions now, but I'm not sure if they were back at the beginning of the year when I first submitted the article. In any case, this meant reworking every figure for fussy things like making sure the pictures were in TIFF format rather than JPG, had a sufficient number of dots per inch, were in CYMK rather than RGB format, and various other things that matter to professional printers. Oh, and printing off a high quality copy on glossy photo paper (in case the digital versions were wonky). Tedious, but fortunately, it didn't take as long as I was fearing.

Second, I spent a fair amount of time worrying about journal abbreviations. For those of you who are not regular readers of scientific journals, referencing is a big deal in several ways. Highly referenced papers are indicative of important findings, and in some places, can be used as evidence for things like promotion. Heck, that I had papers referencing my work was important in proving that I was a bona fide international scientist when I was applying for premanent residency in the United States.

Making sure the reference list is correct is one of the most tedious portions of the writing and proofing process.

Part of this tediousness is that different journals have different rules for referencing. Each one is a punctuation nightmare. For instance, here's how one of my papers might look if it was cited in The Biological Bulletin:

Faulkes, Z. 2006. Digging mechanisms and substrate preferences of shovel nosed lobsters, Ibacus peronii (Decapoda: Scyllaridae). J. Crust. Biol. 26: 69-72.

Here's the same one as it would appear in Brain, Behavior and Evolution:

Faulkes Z (2006) Digging mechanisms and substrate preferences of shovel nosed lobsters, Ibacus peronii (Decapoda: Scyllaridae). J Crust Biol 26:69-72.

And here it is in The Journal of Experimental Biology:

Faulkes, Z. (2006). Digging mechanisms and substrate preferences of shovel nosed lobsters, Ibacus peronii (Decapoda: Scyllaridae). Journal of Crustacean Biology 26, 69-72.

Each one is just a little bit different. But I want to draw your attention in particular to the name of the journal this article was published in. I daresay that few journals list the entire name of a journal in the references; instead, most use some sort of abbreviation. I think the original idea was to cut down on the number of printed pages, and possibly even the number of letters a typesetter had to set. Before the advent of computers, typesetting was a highly specialized craft.

Looking above, you'll notice that one journal abbreviates with periods, another without.

That's the easy difference.

But think about this a little further. This journal has a fairly struaghtforward name. Still, why is it "J Crust Biol" instead of "J Crust Bio" (no "L" at the end)? For that matter, how do you decide how to abbreviate some really obscure journal, or one that is published in a foreign language?

It turns out that there are massive lists of journal title abbreviations. Actually, make that competing lists of abbreviations. There's one standard called MEDLINE for medical related journals. There's an abbreviation standard that used to be called ISI. Apparently there is a World List of Scientific Periodicals which also has abbreviations. And those are just a few that I'm aware of from my dealings in biology. Heaven only knows what the chemists or engineers do, let alone people in the humanities.

The journal that I am submitting to asks for BIOSIS abbreviations (except they list a few exceptions to the way BIOSIS abbreviates, adding even more complexity).

How do you get a list of BIOSIS journal abbreviations?

You have to buy it.

This is around the point where my head starts to hurt. It strikes me as completely bizarre that abbreviations are a commodity (hence my title for this entry).

Many have remarked on how more and more, people are being restricted from doing things because of intellectual property concerns. For an excellent discussion of this, you could do worse than to listen to "Free Culture" presentation by Lawrence Lessig, then head over the Creative Commons website.

Science is supposed to have been about sharing of ideas. Obviously, there are various limits to that, but I'm still trying to figure out how we've ended up in the weird situation where I can't get information I need to write a paper properly, or even figure out what journal something was published in if it was abbreviated.

Why make something harder to understand by using cryptic abbreviations? Are there still some great hidden advantage to using abbreviations in the digital age? Do we save that many pages, or time, or effort?

Journal abbreviations are broken.

One solution is blindingly obvious, of course. Don't abbreviate journal titles. But are editors and publishers willing to take the lead?

Coming soon: My rant against "et al."

23 August 2006

Back in place

New UTPA logoThe trip to Science Park was reasonably successful on several levels. Got some new slides for a manuscript my student Sandra and I are revising; figured out that no, we weren't doing anything stupid on our techniques; got to visit my good friend Virginia; saw how the other half lives (that is, saw lots of expensive scientific equipment that we don't have); and the change of scenery was nice.

Meanwhile, there were a whole bunch of meetings which I missed. I am not sad I missed them. Our president Bambi spoke for a whopping two and a half hours at a general university convocation this morning. The convocation saw the debut of the university's new logo.

I am not wild about it. Rectangles around a star. Whooooo.

It's a bland, generic, geometric design. It says nothing to me about the institution. At least the old one had a palm tree, which gave a hint about our location -- someplace warm. The new logo also reminds me of a swastika. Swastikas have a long and honourable tradition in many cultures, but still has bad connotations. But maybe other people won't see any such resemblance.

20 August 2006

Road trip!

In mere moments, I should be off to Science Park to, well, do science. Will be back late Tuesday. A day of meetings and preparation, then classes start Thursday. Never raining, just pouring.

18 August 2006

Start to finish

Sometime in the year 2000, I walked into the Queen Victoria Market and saw one of the seafood stores had live spanner crabs, which I had been very interested in seeing. I bought some and did some experiments with them.

That project was sort of officially laid to rest this last Wednesday. That was the day I got the actual printed reprints from the journal article I published about them in Crustaceana.

So what happened in between?

I moved across the Pacific and got a new job in September 2001. I worked on the manuscript off and on, and finally submitted it to the first journal #1 in May 2005. It was rejected in June 2005, but comments suggested it might be appropriate for a different journal.

Taking the reviewers' cue, I resubmitted that same month. The reprint I received incidated they got their copy on 5 July 2005. The reprint also notes the final version of the manuscript came in 19 October, so the external review, my revisions and corrections, and editorial decision took about three and a half months.

From there, the paper was actually published in the February issue of Crustaceana, but I didn't see anything in electronic form on the web until May 2006. I'd be interested to know when libraries actually got their copies in the mail. And that makes another three months from online publication to printing and shipping of actual reprints.

Coincidentally, I also finally received a copy of Crustacean Experimental Systems in Neurobiology. I have a chapter in that book, and it was published four years ago now. But it has an average price tag for specialty academic books (triple digits), so it's not the sort of thing you go out and buy on a whim. Buying it was a little reward to myself I got with the money I got for teaching a grad class this summer.

11 August 2006

One more year

I got the paperwork appointing me for the 2007 fiscal year today. And I got a 3.3% raise. I think that's above inflation, except maybe for gasoline.

Meanwhile, I've been spending most of the day thinking about undergraduate research, as I am banging away on the fourth attempt to land an NSF Research Experience for Undergraduates grant. Three other times, they liked it and encouraged revision and resubmission. That I'm writing it a fourth time is a testimony to the triumph of hope over experience.

09 August 2006


As an academic, you're a professional expert. But sometimes you think, "But why does this take so long?" Bachelor's degree, graduate work, post docs more often than not. One answer may be because that it takes about ten years of hard study to become truly expert in anything, according to this article in Scientific American online.

That's the bad news. The good news seems to be that innate talent doesn't seem to be the deciding factor in developing expertise: continued study is.

On a somewhat related note, expertise -- not to mention passion and intelligence and lots of other good things -- are on glorious display at the TED website. The talks are wonderful, sometimes astonishing, must visit links. The blog has plenty of excellent tidbits as well.

04 August 2006

Another week, another talk

Yesterday we had our first symposium for our HHMI students. We're just finishing up the second year of a four year undergraduate research grant funded by the HHMI, and this was something we'd said we'd do. The first year, we were just getting geared up and so it didn't happen. But it went reasonably yesterday.

There were ten students who gave presentations, with a couple of double acts. Some were students who'd already been in the program, and some were just starting. My student, Veronica, gave hers in the afternoon and was fine. Even though her moron supervisor (me) gave her a mislabelled slide. For the record, I know that morula stage comes before gastrula, not after. I can make fun of myself now because luckily, if anyone caught it, they were too polite to mention the gaffe during the talk.

I also found out a few other things that I'd not been completely aware of. Like, that we have a dedicated webpage about our HHMI program. Also found out about some of the stuff going on in our core lab facility, and toured our big mobile lab bus for the first time. The bus is a working molecular biology lab on wheels, which goes out to schools to show kids things like DNA technology. They've already had something like 5,000 kids go through it since it started earlier this year.

We also brought back three previous seminar speakers to provide evaluations of the program. And they took that role very seriously during the day, before they went out drinking -- I mean, to dinner -- with us that night.

If I had a nickel...

Bison nickelIn 2005, the United States put a picture of North American bison on their nickel. It wasn't the first time they'd done so -- it had been on the nickel back around the 1920s. The U.S. Mint did this was done to commemorate the Lewis and Clark expedition.

I got to thinking, though, about how the bison represents just how much of an ecological disaster the settlement of North American caused. Bison, of course, used to be incredibly abundant. They numbered in the tens of millions (here). In the 1800s, they were brought to the verge of extinction. Fortunately, things were -- maybe not put right exactly, but at least outright disaster was averted for bison.

I wonder if the U.S. Mint ever thought they would be commemorating a huge ecological mistake. It would be like putting cod on Canadian coins. Or, if you wanted a social equivalent, like putting slave ship on a coin. There's another big mistake that played a significant role in American history that is no longer done. Somehow, I don't think the U.S. Mint would have put that image on a coin.