Tag Archives: writing

Tools of The Trade: The Laptop in My Pocket

Last Monday, the night before I was due to cover a big conference, my nearly brand-new MacBook Air died: suddenly, completely, and unrecoverably. After hurling a stream of expletives in the general direction of Cupertino, I paid a visit to the Apple store conveniently located next door to the conference hotel. They confirmed that my MacBrick was really most sincerely dead, but there was no way they’d be able to fix it before the end of the conference.

Before leaving the store, though, I picked up a Bluetooth keyboard. That, plus my iPhone and a few other items I already had with me, became my new laptop. I was amazed at how well the arrangement worked, and also at how many people came over to comment on my setup. Here’s what it looked like:

iPhone: the new laptop.

iPhone: the new laptop.

I used the Pages iOS app ($9.99), a standard tabletop tripod (about $10 at any photo store), a Gary Fong iPhone tripod adapter (ridiculously overpriced at $20, but much better-looking than a duct-taped binder clip), and an Apple Bluetooth keyboard ($69).

Considering its $110 price tag, it’s a surprisingly capable system. The Pages app stores files on the iCloud service, so they’re automatically backed up and accessible from anywhere. The keyboard is very quiet and has a feel I’m accustomed to, and the tripod adjusts to hold the phone at whatever angle I need. Of course it also has a built-in web browser, email client, and the ability to install pretty much any other kind of program one might need.

I’m not sure I’d want to rely on this as my only computer on a business trip, but I’ll certainly pack the components for it in case I need a backup again.

Oh, and my regular laptop is once again among the living – my local Apple store fixed it under warranty after I got home.

Tools of the Trade: Timestamps and Text Editors

Quoting people accurately is a mundane but crucial task in my daily work. Over the years, I’ve tried a variety of approaches, but I think I’ve finally evolved the most efficient system for handling it. When I’m conducting an interview or attending a presentation at a research conference, I take copious notes. These used to be on paper, using a complicated note-taking technique I developed in college, but after discovering the amazing capabilities of Emacs (the One True Text Editor), I’ve switched to doing it on a computer.

My notes are not strict transcripts. I tried doing transcripts, but it was more hassle than it was worth, and I found that there’s a conflict between transcribing someone’s words accurately and actually understanding what they’re saying. Instead, I note the important parts of the conversation as if I were attending a lecture, and periodically insert a semi-transcribed snippet if they start saying something I think might be quotable. Such a snippet might read “thr’s bn a lotta contrvrsy n th fld abt this, bt itot tht th mech is rly simpl.” With that sort of primitive shorthand, I can transcribe even relatively quick talkers with about 90% accuracy in short bursts. But I want 100% accuracy.

To get that, I record all of my interviews and conference sessions. Yes, recording phone conversations is completely legal everywhere, as long as you ask permission first. The notes plus the recording give me all the information I need, complete with 100% accurate quotes. To streamline the process, though, I added one more piece: timestamps. As I’m taking notes, I hit a keyboard shortcut, and my computer inserts the elapsed time since I started the recording. When I’m writing, I can look through my notes to find the quote I want, then zip to that time in the recording, play back the tape, and check the quote. Cumulatively, this can shave hours of tedious rewind-play-forward-play searching on a long assignment.

Unfortunately, most word processing software doesn’t offer elapsed time stamps, and because the popular choices are either closed-source (Word, Pages) or mind-bogglingly complicated open source (OpenOffice), it’s not trivial to add this feature. You could sort of work around the problem by using real-time stamps, then calculate the elapsed time between when you started the tape and when you got to a particular point, but that could take as long as just searching the recording blindly. Instead, I suggest switching to a proper text editor (a choice that has a lot of other benefits, too). Once you’ve done that, there are at least two ways to add the elapsed time feature.

For Emacs users, the solution – like the solution to every other Emacs need – is to modify your “.emacs” customization file. It’s not hard. Here’s the bit that does the actual work:

;;; Elapsed time and realtime stamp functions
(defun clock-start ()
"Starts a clock which can then be used by
`clock-insert-elapsed' to insert elapsed time into the current buffer."
(setq clock-start (current-time)))

(defun clock-time-elapsed ()
"Returns the elapsed time since the clock was started with `clock-start'."
(setq elapsed-time (time-since clock-start))
(format-time-string "%T" elapsed-time t))

(defun clock-insert-elapsed ()
"Inserts the elapsed time since the clock was started with `clock-start'."
(insert (clock-time-elapsed) " ")

(defun timestamp ()
"Insert string for the current date and time."
(insert (current-time-string) " ")

To link that to some convenient shortcut keys, also add these lines:

(global-set-key [(hyper f8)] 'timestamp)
(global-set-key [(hyper f7)] 'clock-start)
(global-set-key [f8] 'clock-insert-elapsed)

That’s it. Now, hitting command-f8 inserts a real-time stamp, while command-f7 starts a stopwatch and f8 by itself inserts the elapsed time since the stopwatch started. Whenever I start recording a phone call or conference talk, I simply hit command-f7 right after pressing the “record” button. Whenever the source says someting potentially interesting, f8 then bookmarks it for later access. These keys are convenient on a Mac – if they’re already assigned to something else on your system, simply choose different shortcuts. Once you’ve used them a few times, they’ll become second nature.

For other text editors, I use a pair of Bash scripts that I can call from a general system-wide shortcut. These are incredibly primitive scripts, and I’m sure there’s a more elegant way to do this, but here’s my approach. First, we have a script to start the clock, creatively named starclock.sh:


if test -e ~/Desktop/clock
rm ~/Desktop/clock

echo $(date +%s) > ~/Desktop/clock

That saves a file to my desktop with the current time, in seconds since the Unix epoch date (don’t ask – it works). The other script, etime.sh, looks like this:


BEFORE=$(cat ~/Desktop/clock)
AFTER=$(date +%s)

# Calculate elapsed time in seconds and subtract 19 hours (68,400 seconds)


echo -e $(date -r $ELAPSEDSECONDS +%H:%M:%S)

That reads the clock start time from the desktop file, then calculates and returns the elapsed time since the clock started. Set a pair of keyboard shortcuts (such as command-f7 and f8) to call these two scripts and insert the result of the latter into your text document, and you’re all set. This has worked well for me in both Vim and the free version of Smultron, but any text editor that can call command-line scripts should be able to handle it.

Yes, I understand how useless this post will be to most of my readers. If you’re a scientist working in the lab, you probably have no need of timestamps or interview recordings. If you’re a journalist, you probably have no clue how to make a text editor execute a script, how to modify your .emacs file, or even whether any of this is safe. However, I hope it provides a good example of why you might want to learn those things. For modern writers, editing text on a screen is a fundamental job skill, and the software we use to do it is an essential tool. If you’re limiting yourself to corporate-oriented word processors, you’re like a photojournalist trying to shoot an assignment on a crappy camera phone. It might be possible, but it won’t be easy. Text editors are the digital SLRs of writing, and learning how to use and modify them is time well spent.

Tools of The Trade: Zotero

If you read a lot of scientific papers, or do any other kind of academic study, you need a way to manage the mess. I’m talking about the piles of photocopies, books, and notes – or these days, gigabytes of PDFs, web links, and text files. Zotero is the best solution I’ve seen for this so far.

The genius of this little browser plug-in is that it automatically senses certain types of web content, such as research journal articles and bibliographic searches. It has a particularly profound understanding of PubMed, the main search engine for biomedical science. Zotero doesn’t flaunt its knowledge, though – it just adds an unobtrusive icon in the address bar when it understands what you’re reading. Click that, and you can add citations to a library the program maintains on your computer. There’s also an option to synchronize those citations across other devices, using Zotero’s server. All of this is free.

Zotero in action.

Zotero in action.

Once the citations are on board, you can get to work. The screenshot shows a paper I was reading today. The top part of the screen is the regular browser window, with a paper I was reading online. The bottom section is the interface for Zotero. With a click, I can make Zotero take up the whole screen, or open in a separate window, or go away entirely. To save clips of text from the paper, all I have to do is highlight some text, right-click to get a contextual menu, and then select “Add to Zotero note.” The clip gets stored alongside the citation for easy reference. Of course I can also add my own notes, and can export the notes, the citation, or both in a wide range of formats. There’s also a slew of collaboration tools that operate through the program’s web site.

As with any sophisticated tool, there’s a bit of a learning curve, but so far I’ve been able to figure out how to do just about everything I’ve wanted to with the application. If I find myself thinking “Zotero should be able to do that,” a few minutes of clicking around usually reveals that it can. There are other citation managers available, of course – Mendeley and CiteULike both have dedicated followings – but for what I do, Zotero has been a good fit.

Tools of The Trade: Stand-Up Desk

This is the first of what might turn into a series of posts about tools and tricks I’ve found handy for my work. I figured I’d start with the thing most people would notice first on walking into my office: my standing-height desk.

I switched to working on my feet in the summer of 2010, so if you’re wondering whether I stole the idea from ├╝ber-geek Gina Trapani, I didn’t. While I was ahead of that high-profile example, I’m hardly a pioneer.

In my case, the desire to stand grew out of a simple need for a new chair. While wasting way too much time shopping for one, I stumbled on the stand-up desk idea, and liked it immediately. Rather than buy a new chair, I could simply adjust my desk and dispense with the seat entirely.

Like Gina, I’m fortunate enough to own an Ikea “Jerker” desk, a brilliantly designed piece of furniture that the company has since discontinued. An afternoon’s work raised everything to the appropriate level. Most of the time involved unplugging, removing, then reinstalling my computer and its connected peripherals. I also borrowed a tall stool that was sitting around the house, so I could take occasional breaks from standing while building up my “work legs.”

Standing height desk.

This is where I take a stand.

After the first two weeks, my endurance was up to about four hours. Within a few months, I could stand for most of the day without really noticing. It’s just the way I work. I wasn’t doing this for the exercise, but gained some leg strength nonetheless; my comfortable bicycling pace increased a gear or two. I’ve also lost the pain that used to creep into my spine after a long day of sitting, and my computer is above the easy reach of a six-year-old child, a feature that’s quite handy in my house.

The transition wasn’t painless. I needed the stool a lot at the beginning, and it’s still useful from time to time. I also discovered early on that long periods of standing demand comfortable footwear. My office is uncarpeted, so anything less padded than tennis shoes gets tiring pretty fast. The exact height of the desk also seems to matter more now than it did when I was sitting. Belt height is perfect for working at the keyboard. Writing by hand, however, calls for a surface closer to the bottom of my ribcage, so on the rare occasions when I do that I sit on the stool and lower it a bit.

Overall, I’m quite pleased with this arrangement. I’m not planning to invade Iraq anytime soon, but for the less complex – and generally more successful – projects I do, a high desk works quite well. It seems to make me focus more on what I’m doing and find fewer distractions. In other words, it makes me a more upstanding worker.

How about Walking the Walk?

From the inbox:

Below is information about articles being published in the April 19 issue of Annals of Internal Medicine. The information is not intended to substitute for the full articles as sources of information. Annals of Internal Medicine attribution is required for all coverage

This is off to an excellent start – I’m in favor of reading and linking to primary sources whenever possible, and I’m thrilled to see that a journal is encouraging journalists to do that before they even click on the press release link. I’m ready to give their PR office an A-plus.

Then things go pear-shape. When I actually try to read the full paper, I only get this far:

This item requires a subscription to Annals of Internal Medicine.

Make that a D-minus.

Elementary Textbooks: Now with 24.6% Bullshit

Researchers in Spain recently analyzed the health messages in elementary school textbooks in their country, and classified them based on the level of scientific support for each statement. Their results are disturbing, to say the least:

844 messages were studied. Of this total, 61% were classified as messages with an unknown level of evidence. Less than 15% fell into the category where the level of evidence was known and less than 6% were classified as possessing high levels of evidence. More than 70% of the messages relating to “Balanced Diets and Malnutrition”, “Food Hygiene”, “Tobacco”, “Sexual behaviour and AIDS” and “Rest and ergonomics” are based on an unknown level of evidence. “Oral health” registered the highest percentage of messages based on a high level of evidence (37.5%), followed by “Pregnancy and newly born infants” (35%). Of the total, 24.6% are not based on any known evidence. Two of the messages appeared to contravene known evidence.

Even taking an optimistic view of these data, the “not based on any known evidence” category is pretty disturbing. That means the team scoured a major clinical research database and completely failed to find any study, meta-analysis, or review that supported those claims. If that search by a team of clinicians and public health experts failed, it’s a virtual certainty that the information isn’t coming from some secret trove of amazing science to which the textbook authors had access.

This analysis focused solely on the Spanish-language textbooks used by students in the city of Granada. If nearly a quarter of the health “facts” those students get are simply pulled out of a writer’s ass, what’s the quality of information for students elsewhere in the world? And if the problem is indeed global, as it could be, what are we going to do about it?

One Small Step for NIH, One Giant Terminology Error

I’m sure this will be an interesting and informative talk. I just wish he could have put together a title without abusing the jargon of another field:

Dr. Francis Collins, director of the National Institutes of Health and recipient of the nation’s highest scientific honors, will address the National Press Club at a February 26 Speaker Luncheon. Topic of his talk will be “A New Era of Quantum Leaps in Biomedical Research.” The luncheon was originally scheduled for December, but postponed because of snow.

Once again, for those in the bleacher seats: the word “quantum” is a term of art in physics and chemistry, but it has been widely abused in lay usage. It means the smallest possible change in energy level. Electrons make quantum leaps to higher orbitals in an atom, because they can’t occupy intermediate energy levels. It’s like switching the TV from channel 2 to channel 3 – you can’t put it on channel 2.5, so the smallest possible change is the one you make. If it were even possible to make a quantum leap in biomedical research, it wouldn’t be something to brag about – it would be the smallest possible unit of progress.

Then again, if Collins is going to talk about the tendency of risk-averse study sections to fund incremental projects in narrowly-defined fields, rather than innovative efforts that cross disciplines, his title might be appropriate. But it’s still not something to brag about.

via PR Newswire for Journalists :: All Releases.