Tuesday, February 17, 2015

A Valentine of Science Visualization

Yes I took a picture of my press badge.
Yes I am a big geek*.
The annual meeting of the American Academy for the Advancement of Science (AAAS, pronounced Triple-A-ess) came to my neck of the woods this past weekend, so I coughed up for downtown parking and checked it out. Saturday was full of science and math art, which is right up my alley (when my alley is in my neck of the woods, I guess it's more of a forest path? let's not overthink this) and I ended up falling a little bit in love with space.

The first speaker I saw that day was Horace Mitchell, from NASA's Scientific Visualization Studio. "Scientists have very rich internal worlds," he said. "They visualize things a lot in their minds. We get that out so it excites other people." The studio posts everything they do online for free, "for anyone to use for any purpose." They share thirty terabytes of content every month. Thirty TERABYTES.

It's almost too much to handle; in fact, it is too much to handle and most of it never gets much attention. Remember that "perpetual ocean" visualization everyone was talking about in 2012? It had actually been sitting around on the NASA website since 2011, undiscovered until the studio's social media person decided to tweet about it.

Still from the Perpetual Ocean visualization. Do watch it.
If you need inspiration for anything, artistic or scientific or whatever, I suggest browsing the SVS gallery. It is absolutely one of the best ways to waste time on the internet.

A nontrivial part of the work in making visualizations like this is to understand your audience. In the words of the session moderator, astrophysicist Tom Abel, "For an astronomer blue is very hot and red is very cold. And that would be very bad in the shower."

Mitchell followed this up with an example of the ozone hole. It's impossible to get data on ozone thickness directly above the South Pole, because the sun never shines straight down. The most accurate way to represent this visually is with an empty space. "But that's not the hole," said Mitchell. "The hole is an area of very low ozone around [the empty space]." If an image is only going to be shown for ten seconds on the evening news, the anchor isn't going to explain the difference between "no data" and "ozone hole." An image with an empty space would be confusing, says Mitchell, "So we should interpolate across it."

Speaking of holes and empty space, another astrophysicist, Ralf Kaehler, followed Mitchell's talk with a presentation on dark matter. "First I'll talk about what dark matter is," he said. "We don't know." Showing us an empty black slide, he commented dryly, "It's pretty clear that a direct photorealistic visualization is not a good idea."

Anscombe's quartet: four datasets with identical statistics
 and wildly different graphs. Visualization matters!
Then he went on to show the gravitational effects of dark matter: lensing light and speeding up orbits. And he pointed out that visualizations like these do more than just communicate; they spur improved calculations which feed back into the research itself. One of the other speakers also noted that graphing your data can give you a much clearer picture (har har) than simply crunching the numbers, citing Anscombe's quartet as the classic example.

And in some cases, the image is the data, such as pictures taken by Hubble and its cousin, the Spitzer telescope. No, I'd never heard of that one either. I learned about it in the AAAS Exhibit Hall, where NASA had put up their rather amazing hyperwall for several presentations, including one about Spitzer. This telescope images the sky in infrared wavelengths, which are too long for our unaided eyes to detect. Shorter IR wavelengths pass through dust without being obscured, which provides a much clearer view of the Milky Way than we're accustomed to. But remember, dust is important--stars are made of it. Longer IR wavelengths show you the radiation emitted by the dust itself, and you can see it flowing into the spiral arms of our galaxy, condensing into proto-stars and blowing out into nebulae.

And if love indeed binds everything together (N.B. research connection between love and gravity) then I can't think of a better picture for Valentine's Day.

Infrared view of the Milky Way.
"Star-forming regions appear as swirls of red and yellow,
where the warm dust overlaps with the glowing organic molecules."

* An early version of this post used the word "dork." This error has been corrected by the author's father, who should know.

Thursday, January 1, 2015

How The Ocean Will Kill You, and Other Salty Truths

This article was originally posted on Dan Koboldt's website as part of Science in Sci-fi, Fact in Fantasy—a fun and educational series of blog posts by experts from various fields. Cross-posted here with permission.

The ocean covers 71% of our planet and probably leaks into at least that much of our collective psyche. You can’t dip your toe in a tidepool without getting bitten by symbolism. The depths of the sea are humanity’s unconscious; maritime weather is fickle fate; fish represent Jesus; and the white whale—well, we all know about him.

The ocean has shaped high fantasy like Ursula K. LeGuin’s Earthsea series and hard sci-fi like David Brin’s Uplift books, adventures like Verne’s 20,000 Leagues Under the Sea and thrillers like Benchley’s Jaws.

The immense popularity of these last two titles, however, has contributed to one of the most common misconceptions about the ocean among readers and writers alike.

The ocean can kill you, but probably not the way you think.

When they hear that the ocean is dangerous, most people think of great white sharks, giant squid, maybe even sea serpents. But the most dangerous thing in the ocean is actually . . . water. Because you can’t breathe it.

In the US, about 3500 people die every year by drowning, and half of these occur in what the CDC calls “natural water” settings: the ocean, lakes and rivers. Compare 1750 annual deaths by natural water to less than one by shark (some years there are no fatal shark attacks) and zero by squid (there’s never been a confirmed fatal squid attack).

That’s why real people who work or play in the ocean, like divers and sailors and surfers, take safety seriously and focus primarily on the risks of drowning and exposure. Fictional characters should do the same. The Law of Conservation of Detail may prevent you from waxing lyrical about your kayaking protagonist’s life jacket, but at least you can make sure your divers follow the buddy system.

On the flip side, if you do want to hurt or kill a character in the ocean, it’s tragically easy to find inspiration in real headlines. Operating a boat under the influence. Night swimming alone. Ignoring the dive computer’s warnings.

But I know, I know. Sometimes you just have to threaten your characters with a deadly animal. In that case, may I suggest a cone snail or a blue-ringed octopus?

Most of the animals in the ocean are not whales, dolphins, or fish.

Or even (as much as it pains me to admit it) giant squid. In fact, the ocean is Earth’s premier showcase for the sheer diversity of animal life. It’s got dancing flatworms, sea cucumbers that breathe through their anuses, sailing jellyfish, octopuses that dress up like shrimp, shrimp that can break your thumb faster than you can blink . . . I could go on.

Most of these creatures are invertebrates, animals without a backbone. And some are truly bizarre. In college, my invertebrate zoology professor said that if he had to pick a group of animals that came from outer space, it would be the echinoderms (starfish, sea urchins, and sea cucumbers). Instead of having a left and right side like we’re used to, they have five-pointed symmetry. Instead of a proper circulatory system, they pump raw seawater through their bodies, using the pressure of the water to move their feet. They can regenerate their arms and even their guts. Aliens among us, indeed.

In fact, many writers have drawn inspiration from this realm for creating alien or fantasy life forms. (Writing Outside the Human Box tackled this topic in excellent detail). Marine invertebrates offer an almost endless diversity of shapes, forms and behaviors to stir the imagination.

And if you’re writing horror, try looking up marine invertebrate parasites. Tongue-eating isopods, anyone?

But if you’re not inventing new species or traumatizing your readers, if you’re just writing a few boat scenes or a romantic walk on the beach, do you really need to know about all this biodiversity? Plenty of people who live in coastal towns never see much more than seagulls and the occasional whale. However, it’s worth remembering that today’s ocean is the product of centuries of overfishing.

The ocean we’re used to is unnaturally empty.

Are you writing historical fiction or creating a fantasy/alternate world? Try filling the oceans brimful with turtles and fish twice the size of a person. Pack in the whales like sardines. Consider reading accounts of historical abundance, like this passage from the memoir Two Years Before the Mast, in the year 1834:

We were surrounded far and near by shoals of sluggish whales and grampuses, which the fog prevented our seeing, rising slowly to the surface, or perhaps lying out at length, heaving out those lazy, deep, and long-drawn breathings which give such an impression of supineness and strength. . . . I stood leaning over the bulwarks, listening to the slow breathings of the mighty creatures—now one breaking the water just alongside, whose black body I almost fancied I could see through the fog; and again another, which I could just hear in the distance—until the low and regular swell seemed like the heaving of the ocean’s mighty bosom to the sound of its own heavy and long-drawn respirations. 

On the other hand, are you writing about the future? Consider that whales may become wholly extinct, as in the charmingly cheesy Star Trek IV: The Voyage Home. Sad to say, it’s also reasonable to speculate that we may lose all the coral reefs, sea turtles, and sea birds.

We often think of the ocean as powerful and dangerous. It is. But at the same time, many marine animals and ecosystems are fragile and endangered. To incorporate both aspects in our writing is to give to the sea what we try to give to all of our characters—depth.

Friday, October 31, 2014

An Unexpected Death

Last night I gave a Twilight Zone talk at Creatures of the NightLife, part of the Bay Area Science Festival. It was a lovely experience, thanks to organizers Kishore Hari and Arne Bakker and our hosts at the California Academy of Sciences. The other speakers and I were asked to tell "spooky science stories" based on our research; here's the script I came up with. Happy Halloween!


I am a Humboldt squid.

I heard the deadly click-click-click of a hunting sperm whale. I dropped the fish I’d been chewing and swam for my life. Sperm whales are fast. And no camouflage will save you—they just listen for the echoes of their clicks, bouncing off your body. They have teeth, sharp teeth, but that’s not how you die—it’s the suction when they slurp you down whole.

This time, I escaped. But the sperm whale’s terrible yawn closed on a squid right next to me, and I felt certain I’d meet the same fate one day.

This is the story of how I found a different way to die.

I never knew my parents. I hatched in the open ocean, amidst hundreds of thousands of siblings. Our eyes barely worked, and we were so small that the water felt like thick molasses as we swam.

Every little fish, every drifting jelly, every slightly bigger squid wanted to eat us. I was lucky: I’m the only one of half a million who survived to grow up.

And no matter how much I grew, someone always wanted to eat me. Bigger fish, bigger squids. Dolphins and whales. There was just one safe haven: the breathless deep, a layer of water far below the surface with very little oxygen. Big fish, like tuna and sharks, couldn’t breathe there. But I could.

And so could the little lanternfish, who lived there in huge delicious swarms. It was a buffet, although one that I had to share with all the other squid who’d found the same refuge. I didn’t mind too much—some of the males were very attractive. I began to collect and store sperm for the day when I might lay half a million eggs of my own.

The breathless deep was our playground. It seemed like a great idea to follow as far as it went, so we headed out on migration. We were young and hungry—the world was ours.

We didn’t stay at depth twenty-four hours a day, of course. We followed the lanternfish when they swam up to the surface at night, looking for their own food. And as we migrated north, night by night we noticed the surface water getting colder and colder.

At first this didn’t bother me. The deep water had always been cold, and once I was no longer a baby I didn’t care. But then I began to worry for my eggs. Would I be able to find warm water to spawn ahead, or would I have to turn around?

I pushed the concern aside, because the cold water brought a welcome relief from being constantly hunted. We’d left most of the sperm whales behind, as well as the little boats with glowing lures. And we’d found new food: crunchy rockfish and sweet salmon.

Was it the long exposure to low temperatures that eventually muddled our minds? Or was there poison in the water? I’d heard that algae can sometimes grow toxic, and the shrimp who graze on them become toxic, and if you eat the fish who eat the shrimp then you go crazy and swim out of the ocean to your death.

Or maybe we were simply too eager to sate our hunger. We had been chasing a new kind of small fish. I don’t say they deliberately led us to destruction, but surely they knew better than we how to survive the crashing surf, the shallow beach.

Tumbling and pummeling, hard rocks and rough sand—these were like nothing I had ever felt before. It was all over in minutes, the last waves sucking away from my skin, leaving me stranded.

My powerful body deflated on land. My arms became tangled in seaweed. My gills collapsed. A seagull came to gouge chunks of flesh from my fins. Our eyes met, and I saw him consider how mine would taste. But before he could try a beakful, he was spooked into the air by a long shadow on the beach.

It was a human. The same creature that had caught so many of my kin back in the warm water where I’d been born, and even a few of my companions here in the cold water—for humans, I had learned, are more ubiquitous than sperm whales, and more clever at tracking us wherever we may go.

But this human had no deadly lure, no boat. It stood for a short time, shading my body from the hot sun, probably fascinated by the colors of death rippling across my skin. Then it waved its arms, and another human joined it.

They picked me up, one holding my pecked-apart fins and the other cradling my head. They waded into the surf. And they threw me out into the water.

Survival was no longer an option. I was too damaged by sand and sun, seaweed and seagull. I spent the last minutes of my life rocked by the sea, my vision as blurry as when I was a baby, my broken body as challenged to swim. And I felt something like peace.

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.