Ba-Bopsy

Sep11

“Okay. All my life, I had a lump at the back of my neck, right here. Always, a lump. Then I started menopause and the lump got bigger from the “hormonees.” It started to grow. So I go to the doctor, and he did the bio… the b… the… the bios… the… b… the “ba-bopsy.” Inside the lump he found teeth and a spinal column. Yes. Inside the lump… was my twin.” – Aunt Voula, My Big Fat Greek Wedding

Andrea Martin is a genius, a straight-up acting genius. She was genius on Sesame Street and on Broadway and of course in this movie, and as a result since 2002 I’ve been:

Terrified of any sort of bodily lump
Sympathetic to the plight of vegetarians trying to explain themselves
Aware of the concept of biopsy.

A biopsy is an investigative surgery; it doesn’t kill the subject, but provides information to the doctor or researcher performing the operation. In Aunt Voula’s case, it provided some really unexpected news, and Team Sousa hopes for revelations of the same magnitude (if not the same comedic heights).

That’s right, in addition to our observational data, we’ve started collecting genetic information via dolphin biopsies. Using a special rifle and large, red, sterile, buoyant darts, we (really just Tim, but it’s a team effort) take careful aim at a peduncle (dolphin back, below the fin) and fire, hoping to remove a neat plug of skin and blubber. This sample gets preserved on ice, shipped back to Adelaide, and analyzed to determine the sampled dolphin’s sex and potential genetic relationships.

*This photo shows the whole red dart en route to contact with a Sousa peduncle. The actual sample taken is much smaller (5mm in diameter) and likely couldn’t be seen from this distance.

It does feel like a drastic procedure- I mean, we do actually shoot at the dolphins with a rifle. But the dolphins barely react, generally diving on hearing the noise of the dart hitting skin or water, and then returning to whatever it was they were doing before. (According to Krützen et al., 2002, dolphins react the same way whether they were hit or missed, indicating that it’s really the sound and disturbance of the dart that causes them to duck.) Additionally, the scar created by the biopsy rifle has been observed in several dolphin populations (this method is well-documented and historically proven among people who study cetaceans) to disappear within a month or two. Compared to the gouges and scrapes we see and recognize on Sousa sahulensis and Tursiops aduncus fins, the plug is hardly noticeable.

I don’t advocate shooting anything at dolphins or really bothering them at all (how would you like it?) but short of waiting around for all of our catalogued individuals to turn upside down and wave their genitals through the air, there’s no other way to determine the sex of the various members of our study’s social groups. And the other data (relatedness, genetic distance, etc.) that we will gain will be a fascinating addition to our observations of the fission-fusion groups of mixing dolphins. Do related dolphins spend more time together? How long does a subadult or young adult stay near its mother? Are allied males related to one another?

Most of the time the biopsy rifle stays in its box at the back of the boat. But we’re hoping to collect as many samples as possible to unlock the genetic gold mine that could be present and underlying our Sousa sahulensis’ behavior and environmental needs.

Krützen, M., Barré, L.M., Möller, L.M., Heithaus, M.R., Simms, C., Sherwin, W.B., 2002. A biopsy system for small cetaceans: darting success and wound healing in Tursiops spp. Marine Mammal Science 18, 863–878.

Of Sponges and Bananas and Romance

Aug29

Marine biology is hard. We (scientists!) literally cannot know what our subjects are doing all the time- we (Tim and Team Sousa) are lucky enough to have marine subjects that have to breathe air and come to the surface fairly frequently, but in a rather neat and frustrating exchange they also have a wide home range and can only be spotted effectively during the day, and really only days with good weather. So much of what they’re doing goes unnoticed or unseen, underwater or under cover of darkness or simply when we’re not looking directly at them. Sousa sahulensis has never, to my knowledge, been kept in captivity, nor could we ever say we’d seen them behaving “normally” and/or with a complete range of behaviors if they were to be so kept. Marine biology- it’s like detective work, following incomplete bits of information to try to piece together a whole story. It’s constructing specific questions, ones that we can answer given the limited observations we can get.

However, we’re out on the water as much as we possibly can be- every relatively windless day, five to ten hours at a time- and we see a lot of interesting behavior. For example, “banana pose,” in which a dolphin arches its back, rostrum (nose) and dorsal fin in the air. It’s a goofy-looking behavior, potentially adopted by males as a social or courtship display. Another example is one that I’ve heard about but haven’t yet seen- “sponging,” which in this case* is another potential courtship behavior, in which a male dolphin selects a sponge on the reef (quite a large one, too) and presents it (at the surface, presumably, since Tim’s seen it) to a female. He then adopts a banana pose. How romantic.

I don’t know that I’d consider any of this to be weirder than human courtship behavior, though. If you liked it, then you should have put a sponge on it- what’s the difference? After actually having visited a bar last Friday on my birthday (WHO AM I) I really could not argue for any sort of logic in the ways that young humans choose to behave (and I’m including myself here, don’t get me wrong). Presenting alcoholic beverages to other individuals or groups, rhythmic full-body movements to pre-recorded vocalizations, displays of colors and other physical attributes… Sponges seem more straightforward. Take note, lads.

*”Sponging” can also refer to another really cool dolphin thing- down in Shark Bay, where some other dolphin researchers have been conducting exhaustive focal follows and continuous analysis of several individuals’ behavior, Tursiops aduncus have been seen with sponges over their rostrums, using the squishy animals as shields against anything poky they might encounter while searching the benthos (the bottom, in this case sandy) for food. They actually teach this technique through generations, demonstrating cultural inheritance and general braininess. Ahh, I remember the days when my mom taught me how to forage successfully and keep my nose out of trouble. As far as I recall, grocery store watermelons are supposed to sound hollow, cantaloupes are supposed to be heavy (as is corn on the cob) and most everything else is just supposed to be unbruised. Put my hand under cold water if it gets burned, and while traveling on airplanes, always wear a scarf. Thanks Mom!

Species-ous Allegations

Aug24

As I’ve mentioned before, our focal animal, Sousa sahulensis or the Australian humpback dolphin, has only recently entered the official rolls of described species. In a recent report, scientists named this newly-identified species and thus spake Science- a species was born. Does that sound sort of arbitrary to you? Good, it probably ought to.

Let’s talk about species definitions for a second:

I love species names. I love using those distinct descriptions to identify the organism I’m looking at, and I love the way the fake-Latin words (so science! Very officialness) feel in my mouth. There’s a pleasing elegance to the system through which you can categorize groups of related species, like nested folders or bags-within-bags (kingdom, phylum, class, order, family, genus, species, subspecies). But do I trust species boundaries as absolutes? No, I do not.

A “species” can be defined quite a few different ways, is part of the problem. For example, the biological definition states that for a species to be valid, the population that makes it up must not be able (for reasons of geography, genetic change, or physical incompatibility, among other potential reasons) to produce viable, or fertile, offspring with the group from which it is being separated. Several issues arise with this definition.

First, we consider many animals to be part of one species despite the fact that they’re almost certainly never going to meet and exchange genetic material without the aid of humans. For example, northern and southern hemisphere killer whales in all oceans are still listed officially as Orcinus orca, which is absurd. They can reproduce in captivity, probably, but even groups of killer whales (for example, Southern Residents and the area’s Transients) that live in the exact same bays and straits avoid each other completely in the wild, and probably haven’t exchanged genes for tens of thousands of years. I could go on and on about killer whales and species definitions but I will spare you (for now, mwa-ha-ha) and move on to the next problem.

Second, some domestic animals like farmed turkeys, certain cows, and many dogs cannot reproduce without human assistance. Are they species? They can’t reproduce at all, in reality, so they don’t pass the “fertile offspring” test unless people intervene quite a bit (artificial insemination, cesarean section, etc.).

Some people don’t hold with the biological definition. They prefer to define a species based on the percentage of functional genes that are different between two groups (which varies wildly depending on the age and genetic purity of a presumed species), or physical characteristics that show distance between populations. There isn’t really a definition that captures the flawed system we have (understandably) superimposed on the natural world, and the flawed system doesn’t even capture the nuance that the evolutionary process constantly creates and changes.

Meanwhile, what do you do with mushrooms and plants that can self-fertilize, or other less-identifiable organisms like bacteria, constantly passing genes from one individual to another. How about viruses, just tiny packets of DNA and self-replication machines? People think of things in groups that feel natural (haha, biology = natural…) but that’s not very scientific. It is, however, very convenient and intuitive. We group things to make them study-able, understandable, explainable, referable. For the most part, the species definition really does work to distinguish different types of organisms. We just can’t explain exactly why.

So anyways, it’s a bit tricky to explain why Sousa sahulensis has been officially designated a new group within that system. In this case, a combination of geographic separation, physical characteristics, and genetic difference added up to the split of the Australian humpback dolphins from Sousa chinensis, the Indo-Pacific humpback dolphin. Tomorrow’s post will explain exactly how our Sousa have earned their species stripes- this is likely enough of a biology-nerd’s rant for today.

Stay posted, dearest readers! I’m going to go track down some more cute photos of our resident charismatic megafauna and then turn in- today was long, but wonderful. I’ll dream of manta rays and humpback whales and leaping dolphins- I hope you do too.

Birthday Sousa

Aug22

Yes, today was August 22^nd over here in Australia-land- it seems I get to experience a virtual 36-hour-long birthday since most of my internet-friends are on the other side of the International Date Line and about 12 hours different in terms of time zones. 1.5 times the fun! And I’d say the day lived up to that billing.

This morning we went back to Mrs. Mac’s, Exmouth’s charity-supporting “ops shop”- a secondhand store, carrying everything from coffee mugs to swimsuits to prom dresses to sewing kits, books, and plastic kiddie toys. People drop their junk off and the cool stuff makes its way onto the shelves. Kaja and I have been keeping tabs on their selection of Australian-flag-related clothing (there’s a pretty fabulous bikini that neither of us really thinks we’ll wear, but admire every time we go to the store) and have so far managed to acquire temporary tattoos, blue shorts that proudly display the name of the country across the rear, two small flags, and an Australian flag baseball cap. Get ready, everyone who might expect a souvenir from me- it’s either gonna be a postcard or a recycled treasure from the give-away heaps of small-town Western Australia. Good gracious I love Mrs. Mac’s.

The next stop, grocery shopping, allowed me to indulge in a family tradition that I wasn’t expecting to celebrate. Long-life noodles, boiled and then fried up in a pan- I improvised a bit, since I’m not exactly sure how they’re normally made. Whatever it was that I did turned out pretty awesome though, or at least I enjoyed them thoroughly. With a little veggie stir-fry in a sauce, it was perfect. Or so I thought before Kaja brought out chocolate chip cupcakes, the recipe for which I will need to steal before long.

Then in the afternoon, when the wind died down, we headed out for a few transects on the boat. After a good solid Sousa sighting (research never rests! ADVENTURE IS OUT THERE, and so are Arrow and E, a frequently-sighted and very well-photographed mother-juvenile pair) we came back, wiped everything down, entered data, showered, and headed out for some celebrating.

I can’t think of a better day, though of course I miss my family and friends from home/Dartmouth. Rest assured that I thought of you all (even you readers I’ve never met… I thought of you right now… as it occurred to me that I might have readers I’ve never met… hi?) and wouldn’t have enjoyed this day half as much had it not been for you lovely people, your science, your art, your friendship, your pumpkin bread (hi mom!). Coming up- more science, less birthday, hopefully some diving, perhaps some tropical reef ecology, and YOUR QUESTIONS ANSWERED (if you ask them anyways, I’ll do my best).

FOR SCIENCE AND FOR GLORY,

Agent Red Squirrel

p.s. I’m still accepting contributions to the Vicky-has-Internet Fund- you can message if you’d like to help out. Internets are EXPENSIVE here… and I’d like to keep posting photos and terrible jokes to all you virtual folks! Hooray (and thanks)!

The Science of Sousa

Aug21

Despite all the photos of us smiling and drinking tea on boats, looking at the pretty little dolphins and later playing with baby kangaroos, we are actually here in Exmouth for Scientific Research (note the Important Capitals denoting the Realness of our Science).

Anyways, the research bit is cool too. Out on the boat, we drive transects around the tip of the North West Cape, collecting data on dolphin species, numbers, age classes and groupings, locations, environmental conditions, and the ever-important photographs for identifying individual dolphins from the catalogue Tim’s assembled over the past two years.

We aim for good-quality, zoomed-in, in-focus, and well-lit photographs where the fin is parallel to the plane of focus on the camera and fully out of the water, for maximum potential to identify them. Glare, spray, waves, animal movements, boat lurches, poorly angled light or backlight, focus problems- any of these things and many more can disrupt the camera and leave us with a big pile of crappy photos that we later have to sort through. But occasionally we get a photo like this:

It’s clear and sharp, all four fins are fully out of the water, the lighting and contrast are good, and the dolphins are nearly exactly at a right angle to the direction of the lens. As a bonus, the two farthest dolphins are surfacing “in position,” meaning that their positioning along with the relative small size of the middle dolphin indicates that they are possibly a mother-juvenile pair (or in boat slang, MJ). From this photo, then, we can identify probably three out of four dolphins in the catalogue, note that the group cohesion is less than 2 meters, observe their traveling behavior, determine likely relationships, and enjoy lovely memories of how blissfully flat the water was that day.

When processing this photo, we first zoom in. Most of our photos (not sure about this one in particular) are shot with the lens fully extended to 400mm. We then have to crop out most of the photo, anything that is just water or unidentifiable parts like flukes or pectoral fins. This photo, since it’s got four good fins in it, will be copied into up to five different files, one for each dolphin and one to demonstrate the MJ pair’s positioning and relationship in the water and in the group.

The small fin in the middle (a PJ, or potential juvenile) looks fairly unmarked. The edges are smooth, and though there is some spray obscuring a tiny part of the fin, there don’t seem to be any scars that would last from sighting to sighting and allow us to match this dolphin with photos from another time and place. Dolphins heal absurdly fast and absurdly well, sustaining shark attack wounds and other injuries that would seem fatal to a human while continuing to swim around the friggin’ ocean. And their scars often go away really fast, so they can’t regularly be used to tell one fin from another. Therefore, we go mainly on nicks and notches, the unique shapes and textures of a dolphin’s fin. For example:

In this way-zoomed-in photo, you can see a notch about the middle of the fin, another toward the top, plus two at the tip. By searching the catalogue for a fin with exactly this shape (fairly distinctive, though not nearly the most distinctive fin I’ve seen) we can determine who’s who with relative ease, especially once we get to know the different fins throughout the season. These ones are Tursiops aduncus, Indo-Pacific bottlenose dolphins, not the main study species Sousa sahulensis, and there are more than 250 recognizable individuals in the catalogue, so we probably won’t know all of these really quickly. But there are a few, like “Steps,” that we can recognize immediately.

Her scarring is even more distinctive from the other side, and we’ve spotted her a fair number of times since I’ve been in Exmouth. That’s part of the benefit of photo-ID though- we recognize her every time we see her and her juvenile, but just because the other dolphins in her ever-changing group aren’t as obvious, they can still be recorded and identified at a later and more leisurely (sort of…) time.

So there it is- the first part of the Science! All the analysis and breakdowns of data will come later, as we get even more sightings and process the backlog of photos from past boat days. As a reward for reading all that and hopefully understanding a bit more about why all that foolin’ around on boats and such is important to this study, for you my dear readers I present a really freaking cute photo of a baby bottlenose:

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Boat Days

Aug9

This post is officially dedicated to my uncle Tom, aunt Kailane, and cousins Liam and Aidan! They have most generously contributed to the Vicky-Has-Internet Fund, in addition to being longtime readers and supporters of Agent Red Squirrel. Their questions were about the lay of the land in Exmouth- I know I’ve skipped a fair bit of background in terms of this project and the area I’m living in.

First of all, I’m living in a town called Exmouth, which is on the North West Cape of Western Australia (state bird: the black swan; state flower: the red and green kangaroo paw). I’m working as part of the North West Cape Dolphin Research Project, NWCDRP for “short.” It’s a small town- about 2,200 people here year-round, and since it’s off-season for school holidays in Australia and the whale sharks have mostly moved on for this year, that’s probably a reasonable estimate for the current population. It borders the Indian ocean and the Exmouth Gulf, clearly a sea-oriented town though it appears surrounded by low striated bluffs, red sandy soil, stunted eucalyptus trees, and myriad other dusty shrubs and grasses that shelter ‘roos, emus, echidnas, and other exotic fauna (cockroaches, spiders, ants… you know, cool stuff).

Every reasonably-sized house in this town of reasonably-sized single-family houses and rentals has a boat parked out front, along with some palm trees and plumerias. The more landscaped ones have sunflowers, and maybe a little bit of lawn. But the rainy season is over here, and despite the 30-year flood that washed out levees and kangaroo corpses in town this winter (northern hemisphere’s summer) the ground is dry again. Green grass may not last long as we edge our way into spring and summer.

I’m cooking dinner tomorrow night, so hopefully I’ll have a few more photos of “normal life” here at the house. But for now, here’s what we’ve done in the past few days on the boat:

Since the weather has turned, we have been out from basically sunrise (or slightly thereafter) until sunset (or slightly thereafter). Smooth seas, light breezes, turquoise water with more than 11m of visibility straight to the bottom… life ain’t bad on the North West Cape right now. We load up the boat in the morning, rubbing sleep out of our eyes and sunscreen on our faces, and truck over to one of three boat ramps with the trailer rattling along behind us. Tantabiddi, Bundegi, and Exmouth Marina are our three points of entry, and we motor along from there to wherever our transects for the morning begin.

We science away for a few hours- scanning quadrants of the water and horizon for vessels, whales, obviously dolphins (Tursiops aduncus or Sousa sahulensis, our study species), and anything else that catches our eye. Here’s Kaja science-ing:

Kaja Wierucka

And then we break for a very civilized morning tea.

Sometimes we also break for some penalty push-ups. They’re extra fun when there are swells.

Meanwhile, marine life continues around us. We spot dolphins every few hours, which prompt rapid-fire photography and driving a boat in circles amid much cursing and sometimes ooh-ing and aah-ing (especially if there are calves present); sea snakes aren’t uncommon, nor are breaching humpbacks and calves. We saw a dugong yesterday, and a young hammerhead shark! Tim and I saw Pseudorcas, or False Killer Whales, for the first time today as they came flying by our boat on some unknown mission, spooking two 5-foot sailfish into their wake. I’ve been assured there will be no lack of photographic opportunity, and I’m excited to post more photos for you soon.

Amidst all this ocean nonsense, we make time for lunch and water breaks, but for the most part we spend our time with binoculars and clipboards, searching for the elusive fins and short blows of our dolphin buddies/nemeses. Today as the sun was setting and a mother humpback was breaching in front of the rising moon, we cruised back in to the Bundegi boat ramp. Exhausted dinner, spreadsheet entry, hosing down equipment, blogging, and now sleeping. Lots of stored up good stories for the coming days, plus a special guest appearance by an early-morning dingo and THIS ON THE DASHBOARD OF THE TRUCK:

Yup. This is Australia. Ain’t nobody gonna forget it. Exhausted Agent Red Squirrel signing off- stay happy, readers.

By Any Other Name

Aug2

Scientific names are very important- not only are they identifiers for different species that simultaneously differentiate groups and unify them under larger categories, but they also tend to provide some information about that species, even if the information is the name of a researcher who did seminal work in the area, or that Stephen Colbert is awesome (see Aptostichus stephencolberti and Agaporomorphus colberti, a spider and a beetle respectively named for the comedian).

For instance, upon seeing and naming this new friend:

I can be sure that she’s a relative to someone that long-time Agent Red Squirrel readers might recognize. Nephila clavipes was my research subject in Corcovado, Costa Rica, which is why her legs, which look like the graceful result of some dreadful hair-growing (or hair-shaving) experiments, are so familiar. This lady here is a large female Nephila edulis, which translates roughly to “edible spider who is fond of spinning,” which is illuminating if not entirely explanatory or comforting to the Western palate.

The dolphins I’ll be studying here have been, until I think today, actually, been officially known as Sousa chinensis, but have acquired independence from their northerly cousins and become recognized as Sousa sahulensis. Though not named after me, as they should have been, S. sahulensis do gain potential protection due to their smaller numbers, which brings me to my point: S. chinensis, S. chinensis, wherefore are you S. chinensis? For a research project by any other name would be as wicked sweet. Screen Shot 2014-08-03 at 12.25.46 AM