Or, An Illustrated Guide to Sorting Plankton.

First the motivation: why would you want to spend all summer sorting plankton? Especially why would you go to La Jolla, beautiful warm sunny La Jolla, just so you could sit in a basement laboratory behind a microscope all day--sorting plankton?

Because in 2006 I went on this cruise, and I sorted plankton every night, and my findings were preliminary, but intriguing.
Because as part of this scholarship, I had to do some kind of research collaboration at a NOAA facility.
Because it turns out that NOAA has been doing these cruises, and collecting plankton samples, every few years for decades, and that is an amazing dataset ripe for the picking.
Because it made sense for the fourth and final chapter of my thesis to focus on squid spawning in the tropics, and that means looking for squid babies in plankton.

So, for all of these reasons, I found myself spending the summer in a rather surreal environment . . .

I started a new blog (in addition to, not replacing, Cephalopodiatrist) which may or may not be very short-lived, called Squid A Day. Then I wrote a long post in Cephalopodiatrist explaining why I started the new blog, and whining about the awful UI I had to deal with to do so. Right now I am really excited about writing (I'm throwing my hat in the ring for two science journalism internships in 2010) and art (I'm illustrating my friend Kevin's amazing science card game) and only kind of excited about the act of doing science itself. It's a frustrating situation, because for once, I don't actually hate my thesis--I think it's coming together and making good sense--but I'm so overwhelmingly jazzed about the other stuff that I'm still having a hard time focusing on research.

I will finish this year. I WILL!

Well! I'm finally home from my two-month research collaboration in La Jolla. Any day now (any day! really!) I'll be posting a distillation of my experiences: Plankton Sorting and Identifying for the Layperson. It'll be riveting.

First, though, I'm going to wrap up the unexpected adventures that resulted from a few dozen of my study organisms washing up on the beaches while I was there.

I already wrote about the fun and inky times of finding and dissecting squid on the beach, with the help of some wonderfully enthusiastic chance companions who provided a knife and plastic bags for my samples. Well, they were so grateful--for what was probably the most unappetizing experience of a lifetime--that they insisted on treating me to dinner at White Sands, their (very posh) retirement community. Baffling! But very sweet! Here we are, the squid dinner crew:

The company was outstanding, the food was delicious, and the view is unbeatable--they're right on the beach, watching every sunset over the Pacific. Apparently I'm not old enough to apply for residency, but man, I know where I'm going on Februrary 19th, 2048!

Meanwhile, other people were losing their heads over the whole business--first the squid sensed an earthquake, then they started attacking divers, and wait a minute, they were GIANT squid, weren't they? Actually they were not. Big thanks to Deep Sea News for setting the record straight.

No thanks to the New York Times, who ran the disappointingly sensationalist and poorly-fact-checked AP article, with the addition of this hilariously captioned picture:

John Hyde, a marine biologist, and a jumbo flying squid, now swarming off San Diego.

That is the actual caption--no substitutions, exchanges, or refunds. Was the copy editor so harried that she missed the verb taking two subjects, or was she so entertained that she let it slide? I hope it was the latter.

Finally, the night before I left town, I had the wonderful opportunity to speak about squid to the San Diego Dive Club at their monthly meeting. I started off by introducing all the squid in the area--

 
--but I know more about Dosidicus than the others, so I spent a lot of time skillfully steering the conversation towards that species. It was an awesome discussion; I found the audience was more engaged and curious than those at many scientific meetings. Of course, it was 8pm at the La Jolla Brewhouse--a rather different venue from most conference presentations.

After meeting so many interesting and interested people, I was sorry to be leaving the next day! I hadn't even made time for a dive, just a few short swims and snorkels. Next time I'll get on scuba and look for some squid . . .

For now, it's good to be home, reacquainting myself with the mammals in my life.

If you haven't already, check out the video Trouble in Paradise. I'll wait.

Okay? Now. Take a deep breath and calm down.

The video is a beautifully filmed and narrated work of fiction. Inspired by real events, but fiction nonetheless. Yes, there are Humboldt squid in the waters and beaches of La Jolla. But is it true that "an undersea earthquake has driven these predators close to the shore"? No. Is it likely that local marine creatures "sense an alien presence"--other than divers shining lights in their nocturnal faces? Probably not. And the most important question of all . . .

"WILL ANYTHING SURVIVE THE NIGHT???"

I'm pretty sure there are still octopuses, horn sharks, and divers in the water, along with the squid, so it would appear that the answer is a dull and unequivocal yes.

Humboldt (a.k.a. jumbo, but not giant) squid have been swimming in California waters and washing up on Southern California beaches every summer for years. The biggest stranding events were in 2002 and 2005 and received abundant media coverage, but minor strandings in the intervening years passed pretty much under the radar. This summer's stranding has (so far) been one of the more modest. So why all the fanfare?

Yesterday I had a snorkeling date with a friend at La Jolla Cove (not to be confused with La Jolla Shores, where I was on Saturday . . . La Jollans really like the name of their town I think) so once again I was off to the beach. This time I cleverly brought my own knife, plastic bags, and measuring tape (newly purchased). I also warned the friend that if there were more squid on the beach, science might interfere with snorkeling.

Yes. Of course there were more squid on the beach. There were also more people on the beach--it was a summer Sunday in sunny SoCal, and there was a concert in the park. It was packed. I wish I had a picture of the crowd that gathered as soon as I started dissecting. My extremely patient friend referred to it, not unkindly, as a squid mob.

Just like the day before, it was wonderful and educational, with lots of curious kids and adults, great questions, and so forth. But the best part by far was one woman who came up to me and asked "Were you at La Jolla Shores yesterday?" I said I was. The woman gushed, "You showed those squid to my daughter and my husband and she told me all about it when she came home, she had such a good time! Thank you!"

This sort of thing does wonders for one's self-esteem, but then she went on:

Beach woman: She said you showed them a penis and she got to see where the sperm comes out! She wouldn't stop talking about it!
Me: Is that . . . good?

Apparently it was okay, or at least this particular mother thought it was a hoot, because she was laughing as she told me. She went on to ask me a bunch of great questions about the squid and the strandings.

All the onlookers were eager to inform me that there were more squid just on the other side of the rocks, so I tromped over there and fell in with a most helpful young lady, maybe in her early teens, who guided me over to the squid, took notes on mantle length, sex, and maturity, and asked lots of great questions. Young lady, wherever you are, you rock very much! As does the French family who gathered around, the father translating my explanations for his children.

Father: Poulpe?
Me: Calamar?
Father: Ah, oui, oui! Calamar!

Finally, I saw one fully intact squid in a tidepool, complete with head, arms, tentacles, everything (all the other squid had been partially pulled apart by seagulls and curious beachgoers). But it had clearly been sitting in that tidepool for a very long time and it was horribly putrid. I had a little game of chicken with the onlookers:

Onlooker: If you're going to dissect that, we'll watch.
Me: I'll dissect it if you'll pull it out for me.
Onlooker: Not me. Maybe my son will do it.
Me: Go for it! I'll open it up and you can see what's inside.
Onlooker's son: Yeah, sure.
Onlooker: Really, you're going to get it out for her?
Son: No way.

So that one didn't get dissected, and it is probably still sitting in the tidepool, slowly and inexorably decomposing into primordial ooze.

Oh, and I did eventually get to go snorkeling. GARIBALDI!

And then I put my stomach in the freezer.

For over a month now I've been living in La Jolla, mere blocks from the beach, without having time to touch the ocean. Yesterday I finally got fed up with being too busy to swim, so I just threw on my swimsuit and board shorts and walked straight down the street and into the water. Joy!

After a swim, I took a little walk along the beach to dry off. As I approached the curve of the beach where wave action piles all of the flotsam--mostly kelp and seagrass--I spotted a small gathering of people pointing curiously at something. I went to find out what it was, and possibly offer my services as a marine biologist.

In fact, I had a sneaking suspicion it might be a Humboldt squid, since I'd heard that divers were starting to see them in the water, and I'd seen photos of one washed up on the beach last week. Lo and behold, it was!

I introduced myself: "It is a squid! Hi, I study these! Yes, I study this particular species, and yes, I will study this specific instantiation of it before your very eyes! Wonder and delight!"

Maybe I didn't say all that; I don't remember.

Continue reading and find out how I explained sperm to a  bunch of kids on the beach . . .

(Long-awaited? or long-forgotten? Anyway, here it is!)

October 18, 2006

I've accumulated a number of small cuts and abrasions on my hands from routine lab and field work. They're not noticeable normally, but squid ink is an irritant and makes them red, inflamed, and horribly itchy. Hooray. Still more exotic wound-related news: you know how giant squids leave sucker marks on whales while they're struggling not to be eaten? Well, I try to be pretty careful and stay away from the suckers, but one of the squid got me pretty good the other night, so I have a lovely double row of sucker ring marks on my left wrist. Maybe I should take a picture before it fades.

Bother the squid, all kinds of other excitement has been going on.

Yesterday we crossed the Equator, which I guess I've technically done quite a few times before while flying to the Southern Hemisphere, but it's a very different thing on a boat. The ship has already crossed once on the prior leg of the cruise, and the crossing was apparently accompanied by a grand hazing ceremony for all the "Pollywogs" (people who've never crossed on a boat before). However, that ceremony wore everyone out, so yesterday's crossing was accompanied by little more than a few cheers and the inevitable jokes over the radio. ("Flying bridge, this is the fantail. Can you see the dotted line yet?")

On to the charismatic marine mammals. When a lot of animals are sighted and sea conditions are good, the small boat (a Zodiac, for anyone who's familiar with these things) is launched to chase the creatures down. And yesterday, I got to be a member of the scientific party on the boat! There were four of us--all women--and a crew member who was driving the boat. Of the other three scientists, two were armed with crossbows and one with a camera.

We had launched in pursuit of pilot whales but ended up surrounded by what one of the crossbow-wielders refers to as "white rats"--Tursiops, bottlenose dolphins. Of course I was staring around me in utter delight, trying to keep my jaw out of the water. I was mere feet away from dolphins, wild dolphins, in the middle of the ocean! They are fast and sleek and beautiful, but these words are meaningless compared to the sheer cruising, twisting, jumping
glory that is a dolphin.

What we really wanted for scientific purposes was pilot whales. But since they seemed a lot more boat-shy than the dolphins, we gave up and starting shooting the dolphins. I managed to make myself very useful--I'd be handed a used dart, then I'd unscrew the tip with the sample in it, put it in a bag, label the bag, put that on ice, screw a new tip on the dart, and hand it back to the archers.

After nearly an hour of this (though I hardly noticed the time pass) we finally spotted a group of pilot whales, headed right towards us, swimming in tight formation. They are small, dark whales, often called blackfish, and they are no less beautiful than the dolphins. We managed to get one sample, then headed back to the ship.

October 24, 2006

Today we got a bit of unexpected excitement: we found a couple of turtles entangled in fishing line, and were able to send out a party in the small boat to cut them free. They'd sustained some damage but hadn't accumulated a lot of barnacles, so they probably weren't there very long. We expect they'll do fine, as turtles are pretty sturdy; one of them was missing a flipper from a much earlier encounter, perhaps with a boat or a shark, and seemed to be managing all right.

October 28, 2006

I saw my first sperm whale yesterday evening. Sperm whales (Physeter macrocephalus) are huge, majestic, mysterious, fascinating, and many other adjectives as well. One of those adjectives is frustrating. They're boring to listen to on the acoustic array (click-click-click-click in painfully regular intervals), and disinclined to cooperate with photography or biopsy attempts. Worst of all, the sperm whale protocol calls for ninety minutes of effort by all marine mammal observers for each sighting. That means, when a sperm whale is first sighted, the call goes out: "All observers to the flying bridge" and the observers currently off-duty have to drop whatever they're doing and spend an hour and a half looking for that sperm whale. As I understand it, this protocol has been developed because sperm whales can dive for such a long time. Somebody has calculated that ninety minutes is the optimum amount of effort as far as likelihood of re-sighting, or something like that, anyway.

Last night's sperm whale sighting was cut mercifully short by the sunset. But before that happened, I borrowed some binoculars and get a pretty good look at the beast--well, at his back, anyway. He wasn't exactly jumping and frolicking the way the dolphins do. Sperm whales tend to have a lot of scars, many of them inflicted by giant squid as they're being made into a meal. I would have loved to see a really clear sucker ring scar, but no such luck.

Still, it was a thrill to see the Leviathan, in person.

After evening oceanographic operations and another no-luck squid night, I went out to the bow of the ship with the oceanographer and one of the engineers. We left the glaring, artificial lights behind, and my pupils expanded and expanded, drinking in starlight and moonlight until the shapes of my companions were nearly as clear as they would be in daylight.

The stars were bright, abundant, breathtaking. The moon was remarkable, a perfectly horizontal crescent that looked so convincingly like the grin of the Cheshire Cat that we kept expecting the rest of the animal to pop out of the clouds. We watched it sink towards the horizon, turning from white to yellow to orange, and found that a moonset can be quite as striking as a sunset.

Around midnight, as we headed back in, we stopped to lean over the side and admire the bioluminescence. The waves were breaking off the bow with explosions of light, bright enough to illuminate your face. When I looked ahead, I could see similar explosions, anticipating our arrival. I went to bed filled with awe and wonder.

I think this cruise is the first time I've experience a perfect, unbroken, 360-degree horizon. Not the slightest hint of land breaks the smooth circle around us. It makes the night sky spectacular and rainbows, well-nigh miraculous. One morning, earlier in the cruise, I went up to the flying bridge just an hour or two after sunrise. We were headed into one of those tropical squalls so common in these latitudes. In front of the ship was spread the ideal rainbow, arching perfectly from horizon to horizon, and to one side was a gorgeous sundog, a triangle of color under the clouds.

It quite took my breath away.

October 30, 2006

Well, at just about nine and a half degree north, we’ve kissed the ITCZ good-bye. It can be seen as a dark gray smear across the horizon behind us--so dark, in fact, it looks almost like land. Last night it was pouring rain (tropical rain, the kind with raindrops so big that just one will soak you) and this morning there are blue skies and sunshine ahead of us.

November 4, 2006

After 30 days at sea, being on land again is sensory overload--leading me to realize that living on the boat must have been some form of mild sensory deprivation. I woke up early yesterday; it was still dark outside. The first thing I noticed was the smell. It was different, fuller, somehow, where the scent of the high seas had been pure, scarce, empty. The smell of land in the air was the smell of things growing and decomposing, living and dying in abundance.

The second thing I noticed was a light on the horizon. A light. Out there. It was a shock and a pleasure I can't describe to see something other than vast space.

As the sky lightened, pre-dawn, I saw the origin of the lights. Land. Mountains. Shapes and colors I hadn't seen for thirty days filled my vision. It was glorious, glorious! I was ready to get down on my knees and kiss it, or fling my arms wide and go running all over God's green earth.

But there were still many hours to wait; coming in to port and clearing customs is a slow business. I had a busy morning, packing up my samples, scientific gear, and personal gear. But I made a point of going outside often to appreciate the steadily growing number of available sensations.

Manzanillo is a tropical port, so we passed islands of lush green and smelled all the hot, humid, fruity smells associated with such a clime. I saw people on the beach, and wondered who they were. When I realized I didn't recognize them--they were strangers--I was delighted. I had been seeing the same people for so long that unknown faces were inordinately interesting.

November 5, 2006

I truly believe that in the last seventeen years, I have never seen my cat as happy as she was when I walked in the door and started petting her.

I spent October on this boat, as a visiting scientist for leg 3 of this cruise. The weekly reports make pleasant reading, if you're in to that sort of thing. Progress in each of the cruise's main science pursuits (marine mammal sighting, biopsies, and photography; birding; oceanography; acoustics; dip netting and catching fish) is summarized in the reports by the scientists in charge of each task.

However, if you're interested in a less professional perspective, you can read these excerpts from the journal of a marine biologist who was till recently almost wholly ignorant of marine mammal biology.

October 9, 2006

I just saw three blue whales! They were spotted a long way off, but we chased them until they were right at our bow, and we could look down from the flying bridge at the very top of the ship and see their long, long bodies just under the surface. We could also see three scientists perched at the bow of the boat, two holding crossbows and one, a rifle.

Bizarre, yes. The weaponry is for biopsies. They shoot small darts that nick a little bit of tissue from the animal's hide. The dart doesn't get attached to the animal; it gets reeled back in to the boat, or, if the line snaps (which seems to happen more often than not) we swing around and pick it up with a dip net over the side.

This afternoon, the girl with the rifle (who's one of my roommates) got off a good shot, so we have a sample from one of the three whales. They'll take it back to the lab and analyze its genetics to learn about the population structure of these magnificent beasts.

October 11, 2006

The 9th was an extraordinary day for sightings! I've not had time to write about it until now, but the evening net tows provided a really exceptional animal that I've never seen alive before: a paper nautilus, genus Argonauta. Strange as cephalopods are, argonauts would definitely be in the running if there were a contest for the strangest. The females are quite small--this specimen was thumb-sized--and the males are an order of magnitude smaller than that. Much of the male's mass is one enormously enlarged arm that is used for sperm transfer; it actually detaches from him at the time of mating and swims into the female's body cavity. When these arms were first discovered, they were thought to be parasitic worms.

Not to be outdone as far as strange reproductive habits go, the female uses two modified arms to secrete a shell, in which she lives and broods her eggs, once they are laid. The shells look superficially similar to those of the nautilus in structure, but argonaut shells are much thinner and more delicate. While the nautilus is permanently attached to its shell (it would be difficult to say if the animal is part of the shell or the shell is part of the animal), the argonaut can crawl freely in and out. Ours did this, once we took her out of the cod end of the net tow and put her in a little dish, and I caught it on film. She was beautiful, fragile, perfect.

After the initial discovery, filming, and photography, my net tow companions left me to my evening's work: sorting the plankton tow for squid paralarvae, then processing the squid that were jigged earlier in the evening. Usually the only people I see for the rest of the night are the crew members on duty, who walk regular rounds of the ship to check for fires, drownings, what have you. On this night, word of the argonaut had been passed around, and every crew member who walked through the lab wanted to see it. It was fun to have something to show off.

After sorting the plankton tow and extracting any squid that I find, I freeze the rest; it goes to another researcher somewhere. Then I trot outside and down to the lower deck where I finish with any squid that were caught earlier in the evening. It's a much more exciting venue for dissection that I was used to on the New Horizon. Back on that June cruise, the ship was stopped, the sea was calm, the lights were on, and there were plenty of other people around. But out here everyone else is in bed, the lights have been turned off, and the ship is hurrying along through the whitecaps. On a cloudy night, which is what we've been having, there's no way to tell the sea from the sky. As I stare out I can see only white foam rising and falling at the side of the ship, and beyond that, blackness.

At that point I usually give the obligatory late-night shiver and turn back to the squid on my dissection table (long since killed, quickly and humanely). I remove the stomachs, to study what they are eating and where they fit into the local ecology, and pieces of tissue for genetics, to find out how closely related they are to the squid in Mexico and California. On the night of the 9th, I also removed the gonads of a mature male and female squid and artificially fertilized some eggs so that I can study development and behavior of baby squid.

October 12, 2006

We had an orca sighting yesterday. While I was sitting in the lounge catching a few minutes of Harry Potter, the announcement was heard: "We have killer whales right off the bow, very active, breaching!" So of course we all raced outside, and of course by then there was nothing to see.

But we waited, breathing the fresh air and watching the last colors of the sunset fade from the sky, and then there they were, off to port. They were beautiful! I didn't see any full breaches but I saw a lot of them above the water, and I saw at least one tall, narrow fin of a male orca. Our chief scientist tried a long shot with a crossbow, and didn't get a successful biopsy, but as he very correctly pointed out, "You can’t get a sample if you don't shoot."

(to be continued)