Thursday, September 18, 2014


Behold the completely organic mower!
Make it a gift to your wife to show her
you love the environment and the lawn.
And imagine this: it's always on!
What's more, you'll never need to buy gas
because this machine runs entirely on grass.
Yes, your new mower will be self-sufficient,
consuming its cuttings, neat and efficient.
It also features a decorative appeal.
We're sure that once you see it you'll feel
this South American tool has a place
in your tidy and tastefully flowered space.
Frustrated residents of suburbia,
We offer the amazing . . . Capybara!


Okay, it's a far cry from Sandra Beasley's brilliant Unit of Measure ("Everyone is more or less a master of grasses than the capybara"), but it amused me enough to share.

And it's timely, kind of! California's devastating drought has got me feeling very twitchy about lawns. I sheet-mulched mine a few years ago and put in native plants, and even some of them are giving me an awfully parched end-of-summer look.

Perhaps a poem about a passionately aquatic rodent can be considered akin to a rain dance.

Thursday, August 7, 2014

An Open Letter to Reviewer #2

Dear Reviewer #2,

I want to thank you. Not only did you significantly improve my last research paper with your careful comments and questions, you actually encouraged me to continue working on it.

I also want to ask for your thoughts on this thing called "anonymous peer review." Did you ever feel like we were sitting on opposite sides of a very small island, forbidden from meeting in the middle and forced to communicate by floating bottle? I sure did!

This isn't about time--you and Reviewer #1 were both admirably prompt, returning your comments within a month each time I submitted or resubmitted. (The year and half it took to get the beast revised and published was entirely due to the fact that I gave birth nine days after the first reviews came in, officially starting my new job as principal investigator of a longitudinal study of human development [n=1], so I didn't have a whole lot of spare time.)

The paper went through two rounds of review; the first time Reviewer #1 raised "minor points of concern" while you had "more substantial criticisms," as the editor put it. After I revised and resubmitted, Reviewer #1 gave it the thumbs-up, but you had quite a few more questions and comments.

However, you also wrote, "The authors have done a nice job of addressing many of my concerns and have responded to my points in a conscientious and well-reasoned manner . . . Overall, I am pleased with the revised document and appreciate the authors’ hard work in revising the manuscript."*

Those kind words were copied and pasted to the top of my revision document, and I re-read them every time I came back to work.

One of your criticisms had me and my co-authors scratching our heads for a couple of weeks. Finally I asked the journal editor to pass a message to you, asking for a reference or two to clarify your point. The bottle floated to your shore, then back to mine, and I was happy to uncork it and find the needed clarification.

Going through the editor didn't slow things down much, but it still felt silly to me. Why all the fuss about preserving anonymity?

I know that there are valid arguments in favor of anonymity, but I don't think they apply here. Yes, junior reviewers commenting critically on the work of more established scientists can be burned by a loss of anonymity. But I can only imagine how often it happens the other way around--that reviews are biased by reviewers' knowledge of the authors.

Because usually the authors' names are right there on the manuscript.** And when reviewers know names, they can't help guessing gender and ethnicity and probably other attributes, and we all know humans have biases, conscious and unconscious.

Opening up peer review won't make us all angels, but at least it would make us take responsibility for our words. As Richard Smith wrote in an editorial about implementing open peer review at the British Medical Journal: "A court with an unidentified judge makes us think immediately of totalitarian states and the world of Franz Kafka."

The Journal of Experimental Biology, through which you and I corresponded, still has publishing ethics like the majority of journals, which promise that reviewers "will remain anonymous and their comments will not be published."

Were you glad of that? For my part, I think it would be great if your comments and my responses were a matter of public record, as in publishing experiments like PeerJ. You made the work substantially better; shouldn't you be credited?

Not only would publishing research as an exchange between authors and reviewers benefit both, it would also be a service to the public. It would more clearly showcase science as an iterative process, a collaborative, continuous pursuit of greater understanding.

So: what do you think of open peer review? Have you ever participated in it? (I haven't, much as I'd like to.) Would you appreciate acknowledgement of the time and effort you put into my work?

I remain grateful for your help, whether or not I ever find out who you are,


* I realize that publishing your words here may be a breach of ethics, but I've decided to risk it because the quote isn't identifying or incriminating. If you contact me through any channel and ask me to remove it, I will.

** I've only once published in a journal (Fishery Bulletin) that sends manuscripts to reviewers without author names and, frankly, it wouldn't have been too hard for reviewers to guess. I don't work in a huge field. The paper's introduction made it clear whose work we were building on, the methods gave away the expeditions we went on, and a few minutes of clever googling would probably have provided any determined reviewer with our names.***

*** In some cases, a determined author could probably work this trick in reverse. The longer and more detailed the review, the more information is available: what papers does the reviewer suggest that you cite? Could it be one of the reviewers that you recommended to the editor when you submitted? But I contend that reviewers always have a greater chance of anonymity than authors, because authors pour more of their lives into the paper.

Tuesday, June 24, 2014

Life After A Biology Ph.D.

Tenure is forever, but a doctorate is done in just a few* years. Professors with grad students usually have more than one at a time, so it doesn't take an ecological genius to figure out that the professoriate is reproducing at greater than replacement rate. (But see comments!)

As I understand it, breeding Ph.D.s like academic rabbits made sense in the postwar era when academic institutions, and therefore new professorships, were also spawning like mad. But that was a long time ago. Today, there's a glut of Ph.D.s on the market, all fighting against desperate odds to get the only job they're qualified for: professor.

At least, that's the bleak narrative that gets a lot of press. But in fact many of us Ph.D.s didn't especially want to be professors, and we've made our merry way into a diversity of alternative careers, from patent lawyer to high school teacher. The current grad students at my alma mater are curious about these different options, so I thought I'd make a chart**.

And given how few Ph.D.s are going to become professors anyway, let's stop calling these careers "alternative." We're not sad drips from a leaky pipeline. We are delicious slices of pie, RAINBOW PIE!

(click to enlarge)

Notes, of course:

- Postdocs are sometimes viewed as pre-professors, but a postdoc is really the default option if you haven't quite figured out what you want to do next. Plenty of folks who ended up in NGOs, industry, government, etc., did an academic postdoc first.

- The "unknown" academic is a graduate from the nineties whose current whereabouts I've been unable to track down. She was definitely employed at a university at some point post-graduation, though it's not clear whether she was a professor, and she's not on their staff pages now. Mystery!

- Given the depressing data about gender gaps in academia, I'm a bit surprised and quite heartened that female and male Hopkins grads became professors in roughly equal numbers. Of course, as Crabby points out, there's always a chance for other inequalities.

- I hope none of my blather comes across as anti-professor. I'm super proud of all my friends who are kickin' it academy style. That's why your slice of pie is such a nice blueberry color!

- Come to think of it, why doesn't anyone study the seals? They're RIGHT THERE!

* For variable values of "few."

** While I'm culpable of the idea and execution, it could never have been done without the input, support, and mad data-gathering skills of many other alumni. Thanks to the Hopkins grads--you're all stars!

Saturday, April 12, 2014

Tidbits of Tentacles

I fell in love for the first time at age ten when I met a giant Pacific octopus in the Monterey Bay Aquarium. For two hours I watched the slow dance of suckers across the glass, the deep billowing breaths, and most of all the sharp bright eyes that watched me back.

Giant Pacific octopus. (Randy Wilder/Monterey Bay Aquarium)
When we got home to LA, I promptly sold the expensive American Girl doll that I had saved up forever to buy and began looking in secondhand catalogs for a saltwater aquarium. My dad helped me set it up, our local fish store sold me inhabitants, and at school I became The Girl With The Pet Octopus.

Ten years later, my passion undimmed, I embarked on a cephalopod-themed Ph.D. at Hopkins Marine Station. Literally next door to the Aquarium.


How excited am I that Aquarium's latest exhibit is all cephalopods? "Tentacles" opened today, featuring more GPOs, more cuttlefish, plus tropical octopuses and deep-sea octopuses and the most adorable little bobtail squid and dwarf cuttlefish. And how thrilled was I to be asked to write about it for KQED?

It was "almost supernatural fortune," to borrow the words of artist Nemo Gould. He was "approached and asked to do a strange and specific thing that I already wanted to do"--namely, create cephalopod sculptures to complement the exhibit's live displays. You can read more about them in my KQED article, or just visit them in situ.

While researching the story I gathered pages and pages of gripping material; I was totally sucked in. (Sorry!) Some of it went to KQED and some to Squid A Day. But I couldn't fit in either of those posts all the fun stuff I learned about exhibit design. Live animals are the stars, but as it turns out they have quite the supporting cast.

Arcade Games Physical Interactive Displays

When I walked into the Aquarium's workshop, the Eurythmics' "Sweet Dreams" was rocking out over the radio. Maybe half a dozen enormous poster printers were patiently churning out interpretative signs and wallpaper at a much, much slower beat.

Most fabrication of physical materials is done in-house, which means the Aquarium employs quite a few artists and engineers. In addition to designing and printing flat stuff, they build touchable displays--handles and buttons and knobs to grab and turn and push.

For "Tentacles" they put together a demo of jet propulsion. Visitors can pump a 3D-printed squid body through a tank, its jets visualized by bubbles shooting from its siphon. This strikes me as an especially useful display, given that the really active swimmers among squid are disqualified from live display by that very feature.

Video Games Digital Interactive Displays

After visiting the shop, I was taken to see the programmers, busily building with keystrokes rather than lathes. My host turned on a row of monitors to play looped footage of a school of bigfin reef squid while we talked.

Near the end of the conversation, he pointed out something that had completely escaped my notice: the "school" comprised copies of a single individual, edited and staggered in time so any given screenshot would show each copy in a different pose. This wasn't the original plan, but the aquarists, understandably nervous about stressing their display animals, kept the shooting time to a minimum and they only ended up with good footage of one animal. They made it work.

Copying and splicing squid together, though, is less of a challenge than teaching computers to recognize faces. How do you deal with glasses? Mustaches? The coders had to pull it off, though, in order to create a "facial recognition chromatophore display." When you gaze into this screen, it shows your face covered in chromatophores, the skin cells cephalopods use to change colors. And the chromatophores match your facial expression. For example, "look threatened, get blue rings on your face." How do you look threatened, I asked. My host demonstrated by baring his teeth.


I've never gone to the Aquarium to listen to the music. I don't think I could remember a single tune I've heard there. But every gallery has its own score, whether or not you notice it, subtly influencing your experience.

The music track for "Tentacles" was inspired by "Peter and the Wolf"; the exhibit designers wanted an instrument for each animal. Meetings were held, notes were taken, and then an Aquarium delegate traveled to LA and worked with a producer to write the score. Finally, they hired musicians to perform it.

The whole process took 4-5 months, I'm told, and in retrospect I wish I had asked a hundred more questions. Are the musicians hobbyists, students, professionals? Can people make a living doing this? Does the Aquarium ever play parts of the score for test audiences before going live? Which instrument was chosen for each animal, and why?


People come to the Aquarium to see cephalopods and fish and jellies and otters. No one comes to see humans. Still, Aquarium staff can be an integral part of an exhibit, fielding questions and offering a more engaging presence than an interpretive sign. In "Tentacles," a real live person will do a presentation about cephalopod intelligence a couple of times a day. 

Cephalopods, especially octopuses, are widely known as the brains of the invertebrate world. I've found that "Aren't they really smart?" comes a close second to "Aren't they really tasty?" in frequency of questions from the public about cephalopods. Apparently the exhibit team talked about this a lot, and decided to avoid using the word "intelligence" in favor of talking about "adaptation." I think this was because scientists don't really have a satisfactory definition of intelligence. Nevertheless, at least three cephalopod scientists feel comfortable enough with the word to have published Octopus: The Ocean's Intelligent Invertebrate.

Besides, why be so cautious with terminology while shrugging off other biological inaccuracies? Real squid jets do not contain bubbles. Chromatophore patterns do not translate to human expressions. But a real squid jet is invisible in the surrounding water, and there's little of interest in seeing a foreign language, that may not even be a true language, in which you don't recognize a single word. Concessions are made in the name of practicality and accessibility.

I thought at one point I might like to work in exhibit design, but it seems rather daunting now that I know a bit more. I feel lucky that I get to simply write about all the hard work that goes into something like "Tentacles." I wasn't able to attend the opening this weekend; I may not make it down until the end of the month.

When I do, you'll probably find me in the GPO Grotto, gazing at my first love.

Wednesday, March 12, 2014

Why Grad Students Make Great Parents

The most important lesson I learned from grad school was that it's possible to spend six years doing one thing.

This has been invaluable to a new parent. Because you know what lasts less than six years? Babies. Also, toddlers.

That means every related experience will also last less than six years: pregnancy, breastfeeding, diapers, hourly night waking, etc. I've often found these experiences to be pleasant or at least not unpleasant, but when they become challenging, I just have to remember that if I spent six years in the service of this rather unattractive* document:

Reproduction and early life of the Humboldt squid - Staaf, D.J.

then I can spend less than six years doing [whatever it is] for this charming creature:

Product of reproduction by D.J. Staaf and early life thereof

I don't mean to suggest that parenting is over when the kid reaches school age, or that there won't be new and different challenges in childhood and adolescence. But they'll be new and different. And they probably won't last more than six years, either.

I figured a graduate education must have other applications to parenting, so I crowdsourced ideas on Twitbook--I mean, Facetube--sorry, FACEBOOK. As usual, my friends were brilliant, and generous with their brilliance. The first on the list is mine; the rest were inspired as noted. Behold, the

Top Ten** Lessons For Parents From Grad School

  1. Do nothing once that you are not willing to do a thousand times more. This is as true of zooming a toddler around the house in a laundry basket as of sorting plankton under a microscope.
  2. Be prepared to answer the question "Why?" at any time, about anything, suggests Michael O'Donnell. I'd add that your toddler won't accept "Because!" any more than your graduate advisor did.
  3. "Sitting down to a peaceful, uninterrupted, well-balanced meal is a rare experience," says Amber Kerr. If you stop expecting it in grad school, you won't miss it when you're a parent.
  4. Someday you will have a dissertation and a degree. Someday your offspring will sleep all night and use the toilet independently. That day is not this day. Therefore, as Mollie Manier says, "Celebrate the small wins: my PCR worked! The kids are asleep by 9:30!"
  5. She also points out that it's unwise to hope for specific outcomes. Do you want to prove that two species are closely related? Are you expecting your kid to love volleyball? Way to set yourself up for disappointment.
  6. Ellen Garrett Mirus must have seen the university library's copy of Cephalopods of the World that lived on my desk for almost the entire six years, because she says, "Always borrow your books from a library with no late fees." That will be great advice when I can actually make it to a library again . . . 
  7. "Never become a self-declared expert in something (diaper changing, GIS) because then you will forever be the go-to person when that service is needed," says Liz Alter. "And it will inevitably be needed often."
  8. Do not think about how much you would have been paid for certain tasks if you were not a grad student or parent. As John Ott points out, doing these things for free is (ironically) part of your job.
  9. Maybe you've been meaning to write up those awesome results, or teach your kid about inside voices. Then one day you see the same results in someone else's paper, or you cringe at what just got announced to the entire restaurant. Thomas Hayden may be referencing moments like these when he says, "Just because the deadlines are vague doesn't mean that the stakes aren't high, nor that you won't be called to account at a moment's notice."
  10. Often the people around you would be better company if they had a nap, notes Tracy Walters. Sadly, you cannot force someone to fall asleep.

* I did manage to sneak a bit of cute into said document. I hope it's happily coexisting with the 25 tables, 39 figures, and 21 pages of references . . . 

** As decided by me, because it's my blog and I can do that. Many other excellent ideas were also put forth on the 'book.

Friday, March 7, 2014

Side Effects of Living With a Machine Empath

(click for larger image)

[Transcript of my semi-legible writing:

-Hey Anton are you using all the bandwidth?
-Oh er I may I just done something that killed your connection.
-Yeah it's dead.
-Um just give me a couple minutes I'll try to get it back up.
-How about I just go to bed, would that be better?

Postscript: The scanner was hooked up to my desktop, which is Having Issues, so I connected it to my laptop, then remembered I have to download the drivers, and in trying to install them I learned that some libraries needed repair, which led to a whole host of upgrades and . . . my computer still can't talk to the scanner, so I took a photo instead.

Tuesday, January 21, 2014

Calamari Steaks vs. Rings: The life and times of California's squids

This piece originally appeared in OceanBights, the magazine of the Catalina Marine Society, in Winter 2013. Reposted here with permission.

"Guess what we found!" My excited bunkmate woke me from a nap. I was exhausted from babysitting squid embryos all night, and she was wet from blue-water diving in the Gulf of California. I could guess. "An egg mass!" I scrambled out of bed to follow her to the ship's lab, where the rest of the divers proudly presented me with three glass jars full of transparent gelatinous goo and squid eggs the size of rice grains.

Embryos in a Humboldt squid egg mass.
Credit: Steven Haddock
It was the high point of my doctoral research. And it was the blindest luck. The divers weren't expecting to see a Humboldt squid egg mass sixteen meters below the surface on that warm June day in 2006. They'd been looking for jellyfish when they noticed the car-sized blob, studded with at least half a million eggs. (That may sound like it would be easy to find, but it's a mere smudge in the gargantuan vastness of the open ocean. And a fleeting smudge at that--it may last no more than a week.)

Of the many squid scientists on board the R/V New Horizon, the egg-filled jars came to me because I was the one obsessed with baby squid. Up until then, I'd been generating all my babies in vitro. A Petri dish on a lab bench is quite a different environment from a big blob in the sea, so I was pleased to find that the egg-mass babies agreed with my artificially fertilized babies about some important things, like temperature.

The water in the Gulf at the depth of the egg mass was warm, about 25°C. I kept the jars at around that temperature, and within hours the eggs began to turn into adorable little specks that squidged through the water, while the jelly disintegrated and sank. Artificially fertilized eggs also thrive at 25°C, developing healthy eyes, arms, ink sac, and so forth, and hatching in less than a week. Based on these and further studies, and maps of ocean temperature, I guessed that Humboldt squid have two main spawning grounds: off the coast of Mexico and off the coast of Peru.

Author with Petri dishes at microscope.
Credit: Ashley Booth
Adults may travel to these spawning grounds from the broader range of the species. Humboldt squid live throughout the eastern Pacific, from Mexico to Chile, with periodic expansions further north and south. In the last decade, Humboldt squid have become regular visitors to California, with occasional appearances as far north as Alaska. However, my in vitro experiments imply that these polar explorers must return all the way to Mexico to have their babies. Egg development slows as the temperature drops, and arrests completely below 15°C.

But that’s just where it starts to get cozy for the babies of another species: the market squid, whose embryos prefer 9-13°C water. California is their perfect nursery. In these cooler waters, market squid eggs take much longer to develop than Humboldt squid eggs—weeks rather than days—and when they do hatch, baby market squid are twice the size of baby Humboldts (although twice the size of a grain of rice is not exactly large).

Curiously, these relationships are reversed in the adults. Grown Humboldt squid are famous for their size, reaching over a meter in mantle length (the length of the main body, excluding head and arms) and dwarfing the typical 10-15 centimeters of market squid mantles. Then, despite their speedy development in the egg, Humboldt squid can live up to two years--a respectable age for a squid. Market squid tap out at 6-9 months.

The two species' reproductive habits are wildly different as well. Scientists may have seen Humboldt squid mating once. We're not sure. We've never seen them lay their tremendous egg masses--and we haven't seen another mass since 2006. On the other hand, most recreational divers in California have seen or at least heard of the spawning grounds where market squid gather by the millions to mate, lay their eggs, and die. Females package one or two hundred eggs into a finger-sized capsule, which they glue to the sand, or a rock, or a weed . . . again and again, until the seafloor is strewn with "mops" of eggs.

A concurrent aggregation of fishing boats takes place overhead, using bright lights and big nets to collect the conveniently assembled squid. At my home lab in Monterey, we would wander out from our offices and count the boats during squid season, keeping a running tally on the whiteboard. Sometimes when we needed some squid for a research project, we would grab a cooler and a small net, fire up the motor of our little Boston Whaler and putt out to visit. "Hello there, we're scientists, we sure do admire how hard you're working, and could we please take a small scoop from your magnificent net?" (It may have been phrased differently; I don't remember the details.) The fishermen were generous and obliging, and that night we would have market squid swimming in our tanks, the females periodically affixing egg capsules to the fake ones a postdoc had made.

Author jigging for Humboldt squid.
Credit: Ashley Booth
Humboldt squid make no such net-friendly gatherings, and must be caught one at the time with a jig and a line. Humans are pretty capable with a jig and a line, though: in 2011, almost a million tons of Humboldt squid were landed, making it the largest invertebrate fishery in the world. Market squid aren't too far behind; they support California's largest fishery of any kind.

Though both Humboldt and market squid live in the eastern Pacific, many are shipped west after being fished. But some stay home, and you may well have eaten them. The mantles of the smaller market squid are cleaned out to make tubes, which are then sliced into the familiar forms of calamari rings. To do the same with a Humboldt squid would make girdles rather than rings; instead, they are prepared as squid steaks.

Popular as they are with human diners, squid are arguably even more popular with other marine predators. Fish, sharks, seals, whales--all are eager to chow down on these swimming protein bars. And squid are equally happy to eat each other. Humboldt squid being so much larger than market squid, it's obvious who would be eating whom. In the past, the ranges of the two species haven’t overlapped much, perhaps partly because their babies prefer to develop at different temperatures. But as Humboldt squid move north, could they threaten California’s biggest fishery?

The answer depends on how the two species respond to a changing ocean. At first, it might seem that Humboldt squid are the clear winners. The ocean is warming, and their eggs prefer warmer temperatures. Meanwhile, their range expansion is thought to be tied to the expansion of low-oxygen zones, a normal part of the deep ocean that has been stable for a long time. Now these zones seem to be growing in all directions, spreading out and getting shallower. Although most large animals can’t stand the low oxygen, Humboldt squid are specially adapted to take advantage of it.

But environmental changes have complex repercussions, and the results aren't so clear as "winners" and "losers." The recent 2009-2010 El Niño caused the Humboldt squid fishery in Mexico to crash spectacularly. The animals may have adapted to their altered habitat by maturing at smaller sizes and moving further out to sea, and as conditions return to normal, Humboldt squid may as well. Market squid also respond strongly to El Niño, which has historically caused declines in the fishery catch. Yet in 2010, fishermen caught so many market squid that they reached the management quota of 118,000 metric tons for the first time. It happened again in 2011 and 2012. The simplest explanation: it's complicated.

Baby Humboldt squid.
Credit: Danna Staaf
Squid are more resilient and responsive than many other animals, thanks to their quick generations, abundant babies, and the ability to migrate. These “weedy” traits might be enough to let squid—or at least some squid—survive climate change, even thrive with it. They also lead some people to consider squid fisheries the ultimate in sustainability, but other people are concerned that squids' quick responses to environmental change could actually make them more vulnerable.

Squids' importance as a food item for so many marine animals and, yes, humans, is enough reason to hope they stick around. But there are other reasons, too: beauty, wonder, mystery. Consider the vast market squid egg beds, piles and heaps and mountains of gently swaying mops, shining white in the green murk (worth braving 9°C water), and the sudden appearance in blue water of a dim gelatinous mass large enough to swim through, filled with eggs so tiny you can barely see the Humboldt squid pulsing inside (worth getting out of bed).