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More mandatory fun

September 25, 2014

As a follow-up to the summer’s odd teaching slides, here are some new examples fresh from this fall’s Anatomy & Physiology course (BIOL 241).

Dr. Alfred Yankovic, Adjunct Professor of Medicine

Red Rover: the nano version

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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 SingAboutScience.org 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.”

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The ties that bind

September 6, 2014

One of my major limitations as a human being, aside from being a picky eater, is that I’m not good with tools.

My dad’s dad taught my dad the basics of woodworking and such, and my dad would have gladly done the same for me, but I was never that interested. I thought of myself as a smart person, yet, out in the world of 3D objects, my mechanical intuition and ability seemed mediocre. I received a C+ in wood shop, my lowest grade ever; I failed my first driving test. Faced with such results, I defined myself more and more as a thinker rather than a doer. It’s an issue I still struggle with today. Even basic tasks like replacing a flat bike tube seem daunting.

Against this backdrop of psychological and mechanical dysfunction, I recently attempted to help my 7-year-old son build a Super Secret Police Dropship (Lego set #70815, featured in The LEGO Movie).

Phil followed the two-volume instruction booklet quite well and only needed me at a couple of points. My main task was fastening the end of a piece of string to one of the set’s 854 pieces.

Given the limited length of the string, my large fingers struggled to tie a double knot. I just couldn’t get the end of the string through the loop a second time. Finally, I held the string in place while Phil pulled the end through using needle-nose pliers.

I savored the moment while Phil completed the remaining 49 steps.

Super secret police dropship

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Go big or go home?

August 22, 2014

I don’t have a comprehensive solution to the obesity epidemic, but I’m sure ads like this one aren’t helping. Is there really a lot of Washington state pride to be found in the act of collectively eating to the point of discomfort?

not full

I suggest the following modification.

We are what?

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Improvised sports, #3: Shooting Ballery

August 16, 2014

Most basketball-related games — Horse, Pig, and Around the World, for example — emphasize shooting. So how can a hoops-minded parent get his kid to practice the less glamorous but equally important skill of passing?

Here’s one approach: challenge the kid to hit strategically placed cones with his passes.

Shooting Ballery 1

Shooting Ballery 2

[Previous improvised sports: Sock-Drawer Basketball and Bomb-Pong.]

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Best Guns N’ Roses reference I’ve ever seen on a college’s home page

August 14, 2014

From Bates Technical College in Tacoma, Washington….

appetite

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Ultrarunners need to stop stigmatizing DNFs

August 6, 2014

Many ultramarathon runners talk fondly of the “ultrarunning community,” a diverse cohort of individuals united in our enjoyment of running absurdly long distances. We talk with each other, cheer for each other, and console each other, as kindred spirits do. We’re like a big, happy family with an abundance of eccentric, aerobic aunts and uncles.

But there’s at least one issue that brings out our petty, mean-spirited side: dropping out of races. We feel compelled to judge those whose performance is recorded as Did Not Finish (DNF), unless the DNF is attributed to a medical emergency or simply running out of time.

A perfect example is provided by Andy Jones-Wilkins. AJW is widely and perhaps rightly considered an inspiring ambassador for the sport of ultrarunning. I’ve met him; he’s a nice guy. But he once wrote a long blog post making insinuations about 5 elite runners (Scott Jurek, Anton Krupicka, Geoff Roes, Dave Mackey, Dave James) who had the gall to drop out of races.

1. Scott Jurek at Western States: I respect and admire Scott Jurek as I am sure most of the readers of this blog do. However, when he simply stepped off the trail at Devil’s Thumb this year a little of that respect drifted away. I would have thought the 7-time winner of WS would have gone a little further, dug a little deeper, tried a little harder, and given a little more before cutting off his wristband. Not to be. He dropped. Hal won. Game over.

2. Anton Krupicka at Leadville: This guy is an icon in the sport and really has not done a whole lot to deserve that status. But, he has won Leadville twice, torched both Rocky Raccoon and American River and this past year broke the Course Record at White River. Nonetheless, he dropped this year at the Fish Hatchery after leading Leadville for 70 miles. My son Logan, a huge Anton fan, was devastated. I know his quads were thrashed and he couldn’t walk another step. But, I recall another immensely talented, iconic Coloradan facing the same predicament back in 2004 and he struggled to the Finish only to ultimately finish the job the next year with a Course Record.

3. Geoff Roes at Miwok: I can’t really hold this dnf against him too much as his 100 mile Course Records during the balance of the year speak for themselves but in the most competitive sub-100 miler in the country I was quite surprised that Geoff cashed it in while still in the lead. I assume he was suffering mightily but a struggle to the finish and an 8th or 9th place finish would have spoken volumes. Maybe next year.

4. Dave Mackey at Western States: Nobody expected this. Nobody. Returning to Western States for the first time since 2004 and seemingly in the best shape of his life most prognosticators saw Dave as the man to beat or certainly a force to be reckoned with. Reduced to a walk on Cal Street he chose to end his day 78 miles from Squaw. I am sure he had his reasons but with Scott dropping at Michigan and Dave at The River, Hal had a cakewalk to the finish. More power to him. And, perhaps, to the rest of us as well.

5. Dave James at Western States: This guy has been incredible this year! On fire, actually. 13:05 100-mile split in Cleveland, a huge Course Record at Javelina, hell, he even did a 14:30 100 miler on New Year’s Eve just for kicks. But, he bailed at the Big Dance, hard. Dropped like a bag of potatoes before he even entered the Canyons. Why? I don’t know. But, to get it right in this sport you need to finish what you start. Hopefully, that’s coming in the year’s ahead.

In the comments, I called out AJW on his judgmentalism:

Losing respect for someone based on a DNF without even knowing (or caring about) the particulars of the situation is just plain silly. AJW, you (and others) make the unfortunate assumption that everyone else should have the same racing goals and values as you (e.g., “dropping out is almost always wrong”). Anton explained in great detail on his blog why he dropped out of Leadville, and if all you can muster in rebuttal is to cite the example of Matt Carpenter, well, that’s exactly the point I’m making. Anton is not Matt Carpenter and should not be expected to behave identically because he has his own goals and his own values.

AJW responded:

I did not intend to pass judgement on Anton for dropping. By all accounts he did the right thing and I know he spent considerable time and energy trying to continue his race…. And, just to be clear, I was not judging Geoff, Dave, Dave or Scott either. I know they all had very good reasons to dnf (stomach, heat, injury, etc…) I was simply saying that, as an observer of the sport and a lover of the sport, I was disappointed that they dnf’d and I was wishing that they hadn’t.

To which I said:

When you say you’re not judging these folks, I’m afraid I don’t quite buy it. “A little of that respect [for Jurek] drifted away” when he dropped out at WS? If you lost respect for him, how can you claim that you’re not judging him? Likewise, regarding Roes at Miwok, “a struggle to the finish and an 8th or 9th place finish would have spoken volumes.” You mean that struggling to the finish would have indicated great things about his character; the obvious implication is that dropping out indicates less-than-great things about his character…. You are indeed judging these people, whether or not you can admit it.

So why am I rehashing a four-year-old argument, aside from being a prisoner of my own ultra-stubbornness and ultra-persistence? Well, irunfar.com (home of a weekly column by AJW, by the way) just posted two pieces on DNFs: Your Ultra-Training Bag Of Tricks: Handling The Dreaded DNF (by Ian Torrence) and To Finish, Or Not (by Jessica Hamel). Both are interesting and well-written, yet both propagate the notion that a DNF is something to be avoided at all costs.

Torrence’s post begins,

Did. Not. Finish. They’re an ultrarunner’s three least-favorite words.

This may well be true. But couldn’t our three least favorite words be … oh, I don’t know … “thunder and lightning”? “Eggplant for dinner”? Sure, dropping out is often a major disappointment, but it’s not always the worst thing that happens at a race.

Hamel writes,

Elite runners are often scrutinized for their decision to DNF, especially when it comes at a time when they appear to be in a decent physical condition. These moments often result in “he/she could’ve walked into the finish” responses from the crowd. If the back of the packers can finish in over double the time and in worse condition, then why can’t elites push through their low moments to avoid a DNF?

The attitude summarized by Hamel is not necessarily her own, but it is prevalent. So I will answer the rhetorical question of why. They can no longer reach their goal of setting a PR. They’re not having fun anymore. They’re saving themselves for another race. They’re saving themselves for a tough upcoming week at the office. There are a million reasons, none requiring validation by a jury of peers. With few exceptions, ultrarunning is not a team sport, and ultrarunners are not professional athletes. The 99% of us who are hobbyists should be free to pursue our hobby in whatever manner gives us the most fulfillment and pleasure. So: can we as a community stop assuming that DNFs are, in general, tragedies of the highest order? Can we as individuals stop feeling so defensive about our decisions to drop out?

I hope so.

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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.

USED TIRS

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More juxtapositions

July 18, 2014

I have a soft spot for oddly juxtaposed teaching materials, e.g., a handout covering both lab-grown meat and the structure of the song “Hound Dog.”

Here are some strange bedfellows that appeared in animal physiology this spring and summer.

2014_06_24_sodium_gradient_border
Above: two ways to convey the idea that most sodium (chemical symbol Na) is outside cells rather than inside.

2014_07_17_Botox_border
Above: Clostridium botulinum toxin, an inhibitor of the salt glands of marine birds … and the facial muscles of wealthy humans.

2014_05_20_Goldilocks_border
Above: In retrospect, this illustration of the importance of blood pressure regulation may have been too oblique.

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The neurobiology of celebrity worship

July 8, 2014

The 5th edition of Biological Science by Scott Freeman et al. includes the following figure.
The Jennifer Aniston neuron.

Summarizing the study (R.Q. Quiroga et al., Nature 435: 1102-7, 2005) on which this figure was based, the textbook says, “Through experience, at least one of this patient’s neurons became singularly devoted to the concept of Jennifer Aniston.”

With this example, the textbook authors raise the issue of whether memories are stored in specific neurons rather than in distributed networks.

Are they are also implying that we collectively devote too many neurons to Jennifer Aniston and not enough to, say, Rita Levi-Montalcini?

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