Archive for the ‘Writing’ Category


Stephen, Be Heard!

September 14, 2014

The Dynamic Ecology and Phylogenomics blogs drew my attention to a new “must-read” article: On whimsy, jokes, and beauty: can scientific writing be enjoyed? by Stephen B. Heard (Ideas in Ecology and Evolution 7:64-72, 2014). The abstract is below.

While scientists are often exhorted to write better, it isn’t entirely obvious what “better” means. It’s uncontroversial that good scientific writing is clear, with the reader’s understanding as effortless as possible. Unsettled, and largely undiscussed, is the question of whether our goal of clarity precludes us from making our writing enjoyable by incorporating touches of whimsy, humanity, humour, and beauty. I offer examples of scientific writing that offers pleasure, drawing from ecology and evolution and from other natural sciences, and I argue that enjoyable writing can help recruit readers to a paper and retain them as they read. I document resistance to this idea in the scientific community, and consider the objections (well grounded and not) that may lie behind this resistance. I close by recommending that we include touches of whimsy and beauty in our own writing, and also that we work to encourage such touches in the writing of others.

To this nicely argued piece, I just want to add a few examples of indifference or hostility to my own attempts at whimsy, humor, and/or beauty.

(1) My grant proposals to the NWRCE and PNWRCE, 2010.

Striving to keep readers with me through the Conclusion section, I wrote:

We believe strongly in the importance of the central goal of this proposal, i.e., linking antibacterial compounds to Burkholderia proteins in a manner that will facilitate validation of new drug targets. This interest in compound-target links is not simply a fetish of the investigators involved in this project; within some pharmaceutical firms, knowing the target of a compound with activity against cells is considered absolutely vital for progressing compounds to leads.

A colleague discouraged me from using the word “fetish” on the grounds that “it reminds me of foot fetishes.” Perhaps she was right, but I kept it in as a tiny rebellion against unrelenting formality.

The proposals were rejected.

(2) G.J. Crowther et al., Identification of attractive drug targets in neglected-disease pathogens using an in silico approach, PLoS Neglected Tropical Diseases 4(8): e804, 2010.

This paper contained numerous lists of possible drug targets. Since one of the pathogens covered was Leishmania (the cause of leishmaniasis), the paper was known internally as the “Listmania paper” throughout 10 months of writing and revising. Meanwhile, we searched and searched for a compelling title distinct from that of our first paper on the same topic … while carefully avoiding the most interesting and evocative bit that we had come up with — i.e., the word Listmania. A coauthor killed the term by arguing, reasonably enough, that a pun about a pathogen might be insensitive to the pathogen’s victims. But a “catchier,” less cautious title might also have raised leishmania awareness more effectively.

(3) G.J. Crowther, The database: an educational resource for instructors and students, Biochemistry and Molecular Biology Education 40(1): 19-22, 2012.

The submitted manuscript included this:

The total manpower behind this website, rounded to the nearest whole number of FTE’s, is 0, so its maintenance is kept relatively simple.

Once the journal’s copy editor got ahold of it, it became:

The total manpower behind this website, rounded to the nearest whole number of Full-Time Equivalents (FTE’s), is 0, so its maintenance is kept relatively simple.

To me, this change reduced the sentence’s rhetorical punch and humor. Yet the edited version was (slightly) clearer, and I knew better than to argue for style over clarity. I reluctantly accepted the edit.

(4) G.J. Crowther et al., A mechanism-based whole-cell screening assay to identify inhibitors of protein export in Escherichia coli by the Sec pathway, Journal of Biomolecular Screening 17: 535-41, 2012.

Our submitted manuscript included the following:

While previous studies had included beta-mercaptoethanol in assay buffers, presumably to maintain cytoplasmic beta-gal in a reduced and active state, it did not appear necessary to preserve beta-gal function under our assay conditions; EC626’s response to maltose was similar with and without beta-mercaptoethanol (Fig. 3). Thus, in performing this assay, the unpleasant odor of beta-mercaptoethanol may be avoided.

A reviewer wrote, “The sentence which includes ‘the unpleasant odor of beta-mercaptoethanol’ is not appropriate.”

Here was another chance to stand up for ever-so-slightly-less-orthodox, ever-so-slightly-less-dry writing. This time I stood my ground and got my way.

“We respectfully disagree,” I responded. “It is a minor point, but the omission of beta-mercaptoethanol provided much relief to the rest of our lab, and this is worth noting.”


Descriptivism vs. prescriptivism: a debate with my 7-year-old

August 1, 2014

tire store

“What is that place?” asked my son, pointing to a tan building at the corner of North 80th Street and Aurora Avenue North.

“They sell tires,” I said.

“Are they good?”

“I don’t know. I’ve never bought tires there.”

“But you do THINK they’re good?”

“I really don’t know, Phil.”

“If you had to guess, what would your guess be?”

“Well, they spelled the word ‘tires’ wrong, which doesn’t inspire a lot of confidence.”

“How did they spell it?”

“T-I-R-S. They left out the E.”

“But you could still read it, right?”

Yes, I could. It was a fair point.



Mumbling towards clarity

May 13, 2014

Here’s a lesson that faculty like me need to re-learn every so often: our assignments aren’t nearly as clear to our students as they are to us.

My biology writing course (ENGL 299C at UW) currently requires the paper described below. It’s a modification of a previous assignment, so I’ve had a chance to polish it. Feel free to admire its elegance for a moment.

If I had passed out this assignment in class, then immediately asked the students if they had questions, I probably would have gotten few to no inquiries, and would have congratulated myself on another masterpiece of lucidity.

Instead, I made the students submit questions about the assignment along with their first draft. Their responses, when solicited in THIS way, suggested danger lurking around every turn of phrase! Would they as reviewers know the identity of the authors? Should the review be written to the authors, or the editors of the journal? If several different methods are used, what constitutes an “experimental strategy”? What’s the difference between evidence and data? If supplementary figures are cited in the references section, should they be considered “previous literature”?

We spent about 35 minutes of class time discussing these excellent questions and many others.

If we want useful feedback from students, we need to ask for it in the right way, after they’ve had a chance to reflect on an issue and are motivated to talk about it.

Paper 2: journal-like peer review (final version)

This “paper” will be a peer review of the article you’ve been reading (Wahl et al. 2013 or Vlad et al. 2014). For this assignment, we will imagine that the Wahl et al. or Vlad et al. manuscript has just been submitted to a journal, and that you have been asked to review it for the journal.

Most review forms ask reviewers to summarize and assess a paper’s hypothesis, the claims and evidence, use of previous literature, and writing effectiveness. You will address all of these issues in the discrete sections listed below. You should keep these discrete in your submission, rather than combining them into a single narrative. As with a real review, your audience is the journal’s editors and the manuscript’s authors. However, note that journal editors are in charge of many articles on diverse topics, and that English is not the native language of many editors and authors; thus, your writing should be clear and straightforward even in this context. Your tone should be somewhat formal, although you can still write from the perspective of a reader (“I was confused by…”) rather than making pompous pronouncements (“This was confusing…”).


Please write 150 to 300 words (1 to 2 paragraphs) that address the following questions.

What is the central hypothesis of this study? (Be as specific as possible. Use one or more direct quotes from the paper to assess whether it is defined clearly.)How was this hypothesis tested in this study? (What was the experimental strategy? What predictions does the hypothesis make?)


Identify the 2 to 4 most important conclusions of this study, and write a paragraph (150 to 300 words) about each. How does each relate to the central hypothesis? What is the evidence on which each is based, and how strong is this evidence? Consider the appropriateness of the organisms chosen, the measurements made, and the data reported. What alternative or additional measurements might have strengthened the evidence further?


Among the sources cited by Wahl et al. or Vlad et al., identify 2 that are especially important. For each one, directly quote (with quotation marks) what Wahl et al. or Vlad et al. say about this source, then rephrase this in your own words to demonstrate your understanding. Briefly state how this source adds to Wahl et al. or Vlad et al.’s paper. Go to the source itself (you should have full-text access to it) and compare it to what Wahl et al. or Vlad et al. say about it. What specific parts of the source (figure/table number, etc.) correspond to Wahl et al. or Vlad et al.’s claims about it? Did Wahl et al. or Vlad et al. encapsulate the source accurately? Briefly explain.


Identify one paragraph in Wahl et al. or Vlad et al. — not the abstract or first or last paragraph — that you think would benefit from rewriting. Use at least 2 concepts from ENGL 299C (reader expectations, omission of needless words, transitions/pointing words, reverse-outlining) to explain the problems that you see. Rewrite the paragraph and briefly explain how your version addresses these problems.


Roger Ebert and the art of grading

January 30, 2014

I didn’t know Roger Ebert, but I miss him.

From about 2003 until his death last April, I faithfully read his reviews of every movie I saw, plus many more.

Why was I so interested in Roger’s opinions? He was smart and funny, but there was more to it than that.

Last month I belatedly recognized another aspect of Roger’s appeal while reading The Elements of Teaching Writing by Katherine Gottschalk and Keith Hjortshoj of Cornell University.

Gottschalk and Hjortshoj advise against grading students’ essays right away. Instead, they counsel, “First sit back and read through each paper receptively, letting it communicate whatever it is trying to say.”

This is how Roger treated movies: as works to be experienced first and critiqued second. In his memoir, Life Itself, he says that he learned this from Dwight Macdonald and Pauline Kael: “I go into the movie, I watch it, and I ask myself what happened to me.”

To be this open-minded is admirable. To stay this open-minded after having literally viewed thousands of films would be almost miraculous.

Roger became the Chicago Sun-Times film critic in 1967. Here he is in 2007, reviewing Alvin and the Chipmunks:

The most astonishing sight in “Alvin and the Chipmunks” is not three singing chipmunks. No, it’s a surprise saved for the closing titles, where we see the covers of all the Alvin & company albums and CDs. I lost track after 10. It is inconceivable to me that anyone would want to listen to one whole album of those squeaky little voices, let alone 10.

Sure, the chipmunks are an easy target. But my point is that Roger stayed through the closing credits, still curious about what might come next and still capable of being surprised.

His review continues:

…Jason Lee stars as Dave Seville, who accidentally brings them home in a basket of muffins, discovers they can talk and is soon shouting “Alvin!” at the top of his lungs, as Chipmunk lore requires that he must.

David Cross plays Ian, the hustling tour promoter who signs them up and takes them on the road, where they burn out and he suggests they start syncing with dubbed voices. Now we’re getting into Alice in Wonderland territory, because of course they are dubbed voices in the first place. Indeed the metaphysics of dubbing dubbed chipmunks who exist in the real world as animated representations of real chipmunks is … how did this sentence begin?

That said, whatever it was, “Alvin and the Chipmunks” is about as good as a movie with these characters can probably be, and I am well aware that I am the wrong audience for this movie. I am even sure some readers will throw it up to me like I liked the “Garfield” movie better. Yes, but Garfield didn’t sing, and he was dubbed by Bill Murray. My duty as a reporter is to inform you that the chipmunks are sorta cute, that Jason Lee and David Cross manfully play roles that require them, as actors, to relate with empty space that would later be filled with CGI, and that at some level, the movie may even be doing something satirical about rock stars and the hype machine.

Does he sound annoyed that he had to sit through this two-star kids’ flick? Not really. He came, he saw, and he noticed some things that amused him and some things that he could grudgingly admire. It’s a privilege to get paid to watch and judge movies, good and bad, and Roger enjoyed it until the very end.

Getting paid to read and evaluate student writing is also a privilege of sorts. If decades pass and I become an old man and I’m still doing it, I hope to be doing it with the patience and good humor of Roger Ebert.


Civil discourse

December 30, 2013

A recent, typically excellent post at Dynamic Ecology addressed the question of “How do you critique the published literature without looking like a jerk?”

While I like Brian and Jeremy’s suggestions, they don’t capture the extent to which perceptions of jerkiness depend on very specific choices in wording, rhetorical structure, etc. I want to emphasize here that small changes can make a big difference in how you are perceived.

Brian and Jeremy did provide the following language/writing tips (paraphrased by me):

1. Don’t make ad hominem attacks.

2. When possible, identify possible solutions to the problems you’ve identified.

3. Don’t heap too much scorn upon one individual paper or scientist if the problem is common to multiple sources.

4. Focus on facts rather than opinions.

To these, I add the following additional pointers for avoiding the label of “jerk.” (Some were taken from A guide for new referees in theoretical computer science by Ian Parberry, which I consider relevant because standards for pre- and post-publication review should be similar.)

5. Define the viewpoint from which you conducted your evaluation. What do you know about and care about? What do you NOT know about or care about? Confess possible biases.

6. Acknowledge the positive aspects of what was done.

7. Be as specific as possible in your criticisms. Statements like “the data in Figure 5 were misinterpreted” are both more justifiable and less catty than “this study adds nothing to the field.” If you are questioning one particular paper, consider your target to be the paper rather than the scientist(s) who wrote it. “What’s wrong with this paper?” is usually a reasonable question to ask, but “what’s wrong with these scientists?” often registers on the jerk-o-meter. Also be specific in providing references. Claiming support from unspecified sources is sloppy and rude, but even incomplete citations such as “Johnson 2012” may be more ambiguous than helpful.

8. Give the most space to the most important problems. Don’t dwell on minor flaws. Harping on spelling errors makes you seem like a jerk.

9. Avoid unnecessarily dramatic language. In a manuscript review, I once identified four problems as “critical flaws.” A colleague noted that my concerns would be just as clear if I used a softer phrase such as “main flaws.”

In compiling this advice, I became curious as to how well I follow it, so I rated my past critiques of Lore of Running by Timothy Noakes, Born to Run (part 1; part 2) by Christopher McDougall, “Metabolic Factors Limiting Performance in Marathon Runners” by Benjamin Rapoport, Wheat Belly by William Davis, and “Misconceptions Are So Yesterday!” by April Maskiewicz and Jennifer Lineback. Results are below.

self-critique of my critiques

By my own reckoning, I’m not a complete hypocrite, but there certainly is room for improvement.


I Hate My Hat

September 30, 2013

This weekend my 6-year-old son and I practiced pronouncing words that do and do not end in “e.” I wrote this poem to help him practice.

embarrassing hat

I hate my hat. It made me mad
To get this present from my dad.

My pal was pale. “What’s that?” he said.
“That big, big gold thing on your head?”

He did not have to be so rude.
My hat’s a dud. I get it, dude!

I want to look my best — but nope!
My pop made me look like the Pope.


A great book for a nonexistent audience

August 30, 2013

The world of children’s music suffers from a constant influx of “regular” musicians who have kids and then decide to do a children’s album — or so laments a friend, anyway. Since these Johnny-come-latelies haven’t made a study of other children’s music, they go for low-hanging fruit (writing songs about all of the usual topics: dinosaurs, brushing teeth, sharing, naps) and make rookie mistakes (like using irony and humor in ways that kids won’t understand).

Not being a professional musician, I’m not guilty of that particular sin. Instead I’ve taken the equally cliched path of fancying myself a children’s book author despite being largely oblivious to the standards of this genre.

My latest work, Leila Z and the Terrible Triplets (the sequel to Cakes by Leila Z!), is an interesting case in point. It’s essentially an adaptation of a math seminar I attended as a freshman at Williams College in the fall of 1991.

Leila Z cover

As a science-for-the-masses guy, I’m proud of this book. It presents the math in a fun, relatively accessible manner without being preachy. And yet, even now that the book is done, I still can’t really define its target audience. The story is too simplistic for anyone over the age of 10, and the math is too hard for anyone younger than that.

For now, I’m billing it as a “mini math mystery for the whole family.”

preference diagram


Lucky v. Good, continued

April 26, 2013

While on the road with Phil last summer, I made up a couple of stories about a police dog named Lucky and a ne’er-do-well known as Upton O. Good.

At the time, Phil challenged me to create a third story about Lucky that included the following elements: a train full of police dogs, an invisibility potion, and donuts for everyone at the end.

For some reason, those elements didn’t initially coalesce into a coherent story. But this week, faced with a deadline to produce something for Phil’s probable future cousins, Phil and I went back to my previous notes and we cranked out the tale below.

The Case of the Disappearing Donuts
for Karen, Melanie, and Parker
by Greg and Phil

The town of Pendleton, Oregon is protected by a police force of smart, brave humans and dogs. They are really good at solving mysteries and catching bad guys. Last year, however, they had lots of trouble protecting their donuts! They might still be hungry today if not for Lucky, the German Shepherd who leads the Pendleton K9 unit.

The first time the donuts disappeared, it was actually kind of funny. The chief was talking about road repairs and traffic changes when someone noticed that the donut plate was empty.

“Hey, Peabody, why didn’t you save some for the rest of us?” quipped Officer Fernandez.

“It wasn’t me,” protested Officer Peabody. “I didn’t eat a single one!”

“Then what’s that white stuff on your shirt?” asked Fernandez suspiciously.

Peabody looked down. “Um … I think that’s whipped cream from my hot chocolate,” he said sheepishly. Everyone else laughed.

At the all-squad meeting the following week, people watched the donut plate a bit more closely. As the chief began to talk, the donuts seemed to float right out of the room, as if a ghost were carrying them! This time nobody was laughing. In fact, the entire squad was too startled to say or do anything until all the donuts were gone.

“What –- what just happened?” said Officer Yamada at last.

“It has to be some sort of practical joke,” said the chief. “Let’s not worry about it right now. Besides, you guys have been eating too many donuts lately. Maybe this is God’s way of putting you on a diet.”

“But what if somebody is using an invisibility cloak or something?” Officer Costa wondered. “They could use it to steal things that are much more valuable than donuts!”

“You mean like whole cakes?” asked Peabody uncertainly.

“Jewels! Money! Computers! Paintings! Cars!” Costa replied harshly. “Things like that, you nitwit!”

* * * * * *

As it turned out, Officer Costa was almost right about the invisibility cloak. Pendleton’s most notorious thief, Upton O. Good, had discovered an invisibility potion, which he could pour on anything he wanted to make invisible. Himself, for example.

Good decided that, before stealing anything big, he would try to understand the potion better by using it on some different objects. One day he made an entire train car of police dogs vanish as they returned from a training session in the mountains. Fortunately, as the dogs got off the train, a rainstorm seemed to wash away the potion’s effects. Another time Good dumped the potion on Lucky, who remained invisible for three days until, unable to do his regular police work, he went for a swim in the Umatilla River.

After climbing out of the river and shaking himself dry, Lucky noticed that he was back to normal again. Why had the river reversed the potion’s effects, just as the rainstorm had done? Suddenly Lucky had the answer: the potion was counteracted by WATER! Now, how could he get the humans to realize this?

Meanwhile, Good had had so much fun making Lucky disappear that he decided to do it again. The next day, Good first used the potion on himself, then snuck up on Lucky at the police station and sprinkled him with the potion.

This time Lucky knew exactly what to do. He went to his water dish, waited until some officers were in the room, barked to get their attention, and dipped his left front paw in the water dish. It appeared again, like magic! Then he dipped his right front paw, and then his rear paws, and then as much of his belly as he could fit into the dish. Gradually Lucky’s whole body came back into view.

“Holy donuts!” exclaimed an officer. “It’s as if the water makes invisible things visible again!” Lucky barked to tell the officer that she was right.

Now that the human police knew about the water trick, it was time to set a trap for the donut thief.

At the next meeting, a large plate of donuts was set out as usual, and the chief started talking in his usual way. But just as the first donut started to move, the officers drew squirt guns and fired them toward the plate. The dogs provided reinforcement by lifting their legs and spraying.

In a moment their old nemesis appeared in front of them, soggy and grumpy.

“It’s Good!” yelled one officer while another raced forward to handcuff him and escort him to a jail cell.

To celebrate the capture, the chief bought a fresh batch of donuts. There were enough for everybody -– even the dogs.

“Hey, where are the Boston creams?” asked Fernandez. He sounded upset, but was smiling.

“You’d better ask Lucky,” answered Peabody. “He’s the best detective we’ve got!”


Dogged pursuit of a bank robber

June 10, 2012

[The following story, created under severe time constraints while driving through eastern Oregon, was inspired in part by the joke “Tall Tail,” which is track #4 on the album Puttin On The Dog.]

The Pendleton police department doesn’t have a lot of officers, but it does have an unusually smart and brave dog named Lucky. So when the notorious criminal Upton O. Good robbed a bank in downtown Pendleton, the police chief sent Lucky to investigate, along with a new officer.

The robber fled into a forest, but it wasn’t long before the officer and Lucky spotted his footprints along the muddy trail. They followed the footprints for a long time and eventually traced them to a large cluster of tall trees with lots of branches and leaves. It was clear that the robber had climbed one of the trees and was hiding there.

“Look, Upton, we know you’re up there,” began the officer. “But it could take us hours and hours to find you and arrest you, and meanwhile you might get cold and hungry. Why don’t we settle this with a quick contest? If you can beat Lucky in a simple three-question quiz, I swear by the statutes of Oregon that I will let you go free. On the other hand, if Lucky beats you, you must let me arrest you and put you in jail.”

The bank robber, not being the sort of person who was smart enough to avoid leaving footprints, agreed to this deal from his unknown perch.

“OK!” shouted the officer so that both Lucky and the robber could hear him. “First question: Does the face of a bearded man feel smooth or rough?”

“Ruff!” replied Lucky instantly. “Oh, come on!” protested the surprised robber.

“Now, Upton, a deal is a deal. Second question: what is the 18th letter of the alphabet?”

“Arrrrrr!” howled Lucky with enthusiasm. “Good grief!” was all the agitated robber could say.

“Last question: Is my wife a boy or a girl?”

“Grrrrrrrrrl!” was Lucky’s immediate growl. “Lucky wins!” yelled the officer.

The robber was quite upset at this point. Being a man of his word, though, he hopped down from his hiding spot and let himself be handcuffed and taken out of the woods.

As the triumphant officer and Lucky returned to the station with the robber in their possession, another officer spoke. “Look, I don’t know what happened out there,” he said to his coworkers, “But I can tell you one thing: I’d rather be Lucky than Good.”


Too much to hope for?

May 13, 2012

In case you missed it, the AP Stylebook recently caved to prevailing usage of the word “hopefully.”

Like the friend who sent me this link, I have mixed feelings. On the one hand, the curmudgeon in me bemoans this further erosion of standards. (What’s next — acceptance of frivolous z’s in words/phrases like “For realz?” and “Whatev’z”?) On the other, avoiding nontraditional use of “hopefully” is really awkward in practice. To quote my father, a writer for most of his professional career:

I gave up trying to work around it, since it forces one to sound pompous (“It is to be hoped,” or “One would hope”). I guess you can say, “Let’s hope,” but that may not sound very smooth or natural. I tend to just say “hopefully,” and put up with intellectual stab of pain that accompanies it.

My dad is not simply a descriptivist, either. In his otherwise complimentary reaction to my 1995 commencement speech at Williams College, he noted that I had incorrectly used “aggravate” to mean “to annoy” (rather than “to worsen”).

Overall, some of these distinctions seem useful to me while others seem trivial. I’ve never been able to work up much concern about the splitting of inifinitives, yet I do have deeply held convictions on hyphens (sadly underutilized in compound modifiers of nouns) and Oxford commas (on which I agree with my friend, who writes, “I’m here, I’m pro-Oxford comma, and I vote!”).

Then there are the more straighforward issues such as lie vs. lay and its vs. it’s. I’m strictly a law-and-order guy on those, with no sympathy for the ignorant. Learn the rules, people! Without precise, clear communication, we have nothing but humbergesse and wogenblunks.