A whole lot of Greek and my big goal for 2018

I took this years ago at the Monterey Bay Aquarium – it’s fishy like my dissertation

Something I haven’t blogged about much recently is my progress towards completing my PhD, also known as my never ending project. Even in person, I avoid talking about it because I’m sick of the whole affair.

To start, an update. Weirdly, about two months before the end of my funding, I got the job I started my PhD to get (yay!). Since then the dissertation has progressed at a snails pace. Plus, I have a superpower for proving things don’t work, which is valuable knowledge, at least that’s what I keep telling myself–want to know 50 ways to not get the right answer, I have a list! Exercising my superpower is time consuming and often frustrating.

To make matters worse, dissertation writing is hard because I keep holding on to a general feeling that I don’t know anything—even when presented with evidence that I know plenty. Never-the-less, I’m still plugging away.

This leads me to my biggest goal for 2018 – get my damn dissertation done

Overall, I find academic writing painful to read. It amazes me that fascinating stuff can be made to sound so dull and tedious. But, it is the expected style, so even my own academic writing has fallen down the boring rabbit hole of passive voice. Early on, I tried to be more interesting with my writing and was edited back to dullness which inspired me to start this blog—a place I could write about what ever I wanted in my own voice.

Today, I’m taking an academic paper I wrote in Word (and has since been published) and converting it to LaTex – a fiddly, but necessary task I’ve been putting off. LaTex is a software package commonly used for academic scientific writing, especially when there is a lot of math (my work has a lot of math, but is not the mathiest work out there). Using it isn’t as straight-forward as a normal word processor—it leans more towards programming. Once I get over the initial hurdles of figuring it out (because I use it infrequently) it frustrates me less than Word and its clones—especially for symbols, formula and figures. And (this is the best part), it will automatically create a bibliography for me.

In the end, this paper will form at least two chapters for my dissertation, and I have at least one more chapter already written and in LaTex. It all counts as progress.

My next post will be about my fiction goals for 2018, which is much more fun to write and hopefully read.

Where I use my day job for crop planning


A vintage French photo**

I study the aquatic world off shore. How ocean water moves and mixes is often reduced to equations full of Greek symbols – I find it fascinating, but typically not relevant to the food producing ecosystem I’ve planted in the yard*. This year is different. I’m gambling on a hot summer like last year and here is why: (a detailed description can be found here and is where I got most of my information)

For those of us who live mid-latitude along the west coast of North America our weather is modulated by the ocean. Prevailing winds blow from the Pacific onto land. Since water holds heat better than land, our proximity to the ocean keeps us warmer than similar latitudes on the east coast (on the east coast the same winds blow from the land out to sea, so they don’t get the warming effect of the water).

In a ‘normal’ year the sun to warms surface waters over the summer. Then in the fall, strong winds create upwelling that brings up cold, deep water to cool the surface waters. The pattern then repeats.

In 2013, oceanographers (not me personally since my work is based in the Arctic) noticed that the surface of the north east Pacific was getting warmer than usual. That winter the winds were weaker, as a result not as much upwelling occurred and the water stayed warm into 2014. This is why last summer was so long and hot. This year, before the summer warming has even begun, water is still warmer than usual. This means there is a good chance that this summer will be another hot one.

Although a hot summer is potentially good news for my home pepper and eggplant production, there is a down side. Upwelling brings food (nutrients) up to where our coastal aquatic inhabitants can take advantage of it. Without upwelling our waters will not be as productive. Also, the warmer waters mean new fish are swimming north.

There are several large scale patterns that occur in the Pacific, such as el Nino, but this warming is something we haven’t observed before. We don’t know why this warming is occurring, or how long it will last, but oceanographers are working on figuring this out.

*there is a surprising number of oceanographers with kitchen gardens. At scientific meetings I’ve swapped seed potatoes, stories of squash harvests and even full-sized wintercress plants.

**photo is from here

Scott Inlet – trawling and long lines

This is the forth installment on my field work in Scott Inlet, Baffin Island. Previous installments can be found here, here and here.

17 Sept 2013 – the ship spent the night just outside Scott Inlet starting out out at anchor, but wind and swell caused it to endlessly rub against the anchor chain. The mate, who was on watch, decided to start up the engines, pull the anchor and motor around for the night. All the while, small chunks of ice butted against the hull right beside my bunk which left me with visions of the sinking Titanic. No sleep was to be had, leaving us all looking rough around the breakfast table in the morning.

Over the course of the day we completed 5 trawls – the first time the Nuliajuk had done a bottom trawl. With each trawl, the turn-around time with the equipment sped up as everyone figured out what they were doing. Each trawl was slightly deeper than the last as no one knew exactly how much cable the trawl net had (it turns out around 900m worth). The catch included: Greenland Halibut, Flounder, Arctic Cod, Polar Cod, Alligator Fish, Snail Fish, Northern Shrimp, Striped Shrimp, other assorted shrimp, 2 species of skate, Hookear Skulpin, Eel Pout, and assorted jellies, sponges and stars. I saw none of the animals as I stayed on the bridge taking notes on times, locations and depths while trying not to get sea-sick (I could have popped down to the lab – but didn’t think my stomach could take it).

For the night, we retreated to anchor in Refuse Bay. It was nice not to have to dance around to get my socks off at the end of the day.

18 Sept 2013 – We took the day to circumnavigate Sillum Island, one of two islands that Scott Inlet branches around. The aim was for me to do CTD casts while the long-lines were being set up for sharks. The occasional depth sounding of the chart didn’t even hint at how complex the bottom topography is, multiple deep pools of 700 m and more are separated by shallower sills. Bumps and dips break the flat of the deeper pockets. Mostly, the depth sound returned a hard signal meaning the bottom was probably rock, but occasionally, the signal would return spread out suggesting isolated muddy patches (or something else).

Against the electric blue of the glaciers, the fresh snow looked dirty. In gullies where glaciers reached the water, calved off chunks floated away. These bergy-bits often sported whimsical shapes reminiscent of ancient monsters or partly submerged houses.

I finished the day with 47 CTD casts over a wide area, downloaded and backed up to three places (I’m mildly paranoid about losing data).

Greenland Shark complete with copepod (shark is on its back)

19-20 Sept 2013 – Over the next two days we fished for Greenland Shark deep within Scott Inlet (it was delightfully calm in the sheltered Inlet, I could set a cup of coffee cup down and not have it instantly spill everywhere). We used a long-line bated with squid for the sharks. A long-line is exactly as it sounds, a several hundred metre long line with shorter lines attached every few metres ending in hooks. Anchors weight down both ends keeping it on the bottom, which in our case was around 600 m. Off of the anchors at both ends were buoyant ropes attached to floats so we could recover everything (both ends in case we encountered a snarl and had to cut the line – then we could start again at the other end). Both days, the whole mess of lines, anchors and hooks was left in the water for 24 hours.

While I was there (shark fishing continued after I left), we caught 14 live shark and several more that had been snacked on. Sizes ranged from 1.6 m (baby size) to over 3 m with a good mix of males and females. We didn’t catch anything else, so why were the shark even there? And what were they eating? The sharks were measured, tagged and tissue and blood samples were taken. The question as to why we needed the centrifuge was answered since the blood was spun to separate out the plasma.

Most sharks had a copepod parasite (Ommatokoita elongata) attached to their corneas. Each parasite dangled a finger-length yellowish egg case from the shark’s eye, no doubt impairing the shark’s vision (but, they live so deep, vision is probably not critical for their survival).

We brought on board a couple of shark heads (the assumption was that other sharks had eaten the rest of them). I took the opportunity to get a close up look. The Greenland Shark doesn’t have flashy teeth like a Great White Shark does. Instead, it has tiny teeth reminiscent of a saw blade or razor wire. These shark bite and twist, effectively removing chunks of its prey. Up close, the teeth looked deadly.

Scott Inlet – Getting to work

The bear looking annoyed with us

This is my third installment about this years field work. First is here, second is here.

A polar bear sleeping on a rock greeted us the first morning in Scott Inlet. The bear wasn’t happy to see us as we rudely brought the ship in close to get a good look at him (a young male). The bear got up and moved further up the slope, casting disdainful glances our way. So far, I’ve seen a polar bear every time I’ve gone to the Arctic.

Steep faces on each side of the inlet bracket the narrow band of water of the inlet. The orange and black stained cliffs are high enough that base jumpers use the area – how they get up the cliffs in the first place baffles me, gaps to climb up were rare and filled with glaciers dripping in slow motion towards the sea. The inlet walls would fit the landscape in ‘Game of Thrones’ north of the wall, or exist in Middle Earth. Off one of the cliffs flows the most peculiar waterfall I’ve ever seen. It cascades off the top, then vanishes mid way down. Does the water freeze into snow? Where does the water come from? Below the water was just as shear – our depth sounder listed depths around 200 m and greater only a short distance form the cliffs.

Cliff face at Scott Island

The inlet appeared strangely devoid of life. A few Arctic Fulmars glided by, but never conglomerated around our ship even when we were offering up a free lunch (excess bait squid). Olive green jellyfish about the size of baseballs bobbed in the water. We knew narwhal were in the area, but never saw them – perhaps our depth sounder scared them off.

In 2012, three lines of receivers to listen for tagged fish, plus my two oceanographic moorings and some marine mammal listening devices were left in the water (to a total of 36). We came prepared to re-install these moorings plus add four additional receiver lines. As a result, the back deck of the ship was consumed with 200lb anchors weighing the aft end down. The first order of business was to deploy a batch of new receiver moorings before recovering any.

Instead of depth contours, the chart only listed a few depth soundings leaving most of the bottom topography to the imagination until mapping could be completed (the Nuliajuk is heavily involved in mapping when not doing our work). Depths for the mooring locations were needed to ensure we used the right type of float (non-compressible floats for the deeper moorings). As we checked depths, I did a line of CTD casts. Then we turned around and deployed a line of moorings. A process we repeated several times over several days.

Once the deck was cleared a bit we began recovering the previous year’s moorings. Each mooring was fixed to its anchor with an acoustic release, essentially a hook with enough electronic brains to respond to a code sent from the surface and open the hook. Attached to the release is a length of rope holding the instruments ending in a float. From the ship, we call the release and have it uncouple – then the instruments are pulled to the surface by the float.

Several of us kept look out for the floats as they popped up. When a float was spotted, the zodiac zipped over and pulled in the mooring then transferred it over to the ship. Once the mooring was on board, we cleaned them up – an easy task as nothing much grew on the mooring lines and instruments. If we had put these instruments in temperate waters we’d be scrubbing matts of seaweeds and mussels off. Instead, there was a light growth of algae that wiped off with a towel.

One of my moorings – nothing fancy

One of my thermistors flooded. When I opened it up the batteries we so corroded I couldn’t read any of the writing on them (batteries were removed carefully avoiding the battery acid). The rest of the instruments were fine. I downloaded each instrument, changed the batteries and re-programmed for a another year. I only briefly looked at the data to check if each instrument worked properly (I’ll spend the next while looking at the data in more detail).

Kevin (another scientist) and I tackled the marine mammal recorders, instruments I had never worked with before that use large numbers of D cell batteries. By actually reading the instructions, we readied most of them for re-deployment. Unfortunately, one instrument needed a specialized wrench, which we didn’t have. The wrench was to arrive with our replacements, so I assume it has been dealt with by now.

The mooring work was a success – all the moorings from 2012 were recovered and more moorings were put out.

Next up, some fishing…

Heading up the Baffin Island Coast

A view of Clyde River from the sea

The first step before heading to Scott Inlet was getting approval from the local HTA (hunting and trapping association) to tag fish, install moorings and collect data. Before leaving solid ground, the four of us (as there is only room for four scientists on the ship) waded through the fresh snow to the HTA office located in a red shack beside the community freezer.

The office was utilitarian, lit by florescent lights and a lone incandescent bulb. An uncomfortably low ceiling made me feel it was risky to stand up tall. Once white vinyl tiles covered the floor. In an economy of surfacing, the same tiles covered the chipped white painted conference table – edges held down with masking tape. Most of the table surface was consumed with a big map of the area. The walls were decorated with maps, a variety of posters including a graphic one on caribou diseases, and a wanted add for narwal tusks from someone in Vancouver who “will pay a good price.” Lined up along the walls were boxes of ammunition, rubber boots, ropes, and bolts of dull coloured fabric.

A few moments later, a group of men and one woman arrived. Introductions were made and we all sat around the conference table. We worked through a translator, an HTA member with good English, to explain our work. The group kept stern faces as we explained how the acoustic receivers work and our interest in the Greenland Halibut and Greenland Shark. The HTA members were very interested in if our instruments affect the marine mammals – an important food source for them. The agreed that knowing more about the local Greenland Halibut would help them in setting up a commercial fishery, a potential income source for the community.

However, they were baffled as to why we were interested in Greenland Shark. To them the shark were at best a nuisance. You can’t eat Greenland Shark without serious preparation as the flesh is toxic and contains high amounts of urea. If you have time, these sharks can be fermented and rendered safe to eat, but this is not something the Inuit traditionally do. Nigel, our shark expert, made a compelling explanation as to why we should care about these shark. I’ve been working with Nigel for a few years, his shark work takes him from Africa to the Arctic and his passion for these animals rubs off on me, so even with cold feet I’m excited to see them. The Greenland Shark are the top predator on the bottom of the polar seas and are needed to keep the ecosystem in balance. The HTA members appeared to remain skeptical, but willing to humor us. Ironically, the HTA chair’s last name translated to English means ‘shark’.

The HTA granted their permission asked for a community wide meeting to show everyone what we had accomplished when we finished. While in Scott Inlet, a local community member was to accompany us to see what we were doing, which has happened in previous years. We were also asked to bring back some Greenland Halibut back for the community and to take supplies to a group of hunters stranded in Scott Inlet. After the meeting, we begged a ride (there is a taxi in town, but its availability is never certain) to get our gear down to the water’s edge and then transferred to the Nuliajuk (the ship).

We couldn’t leave until the next afternoon as gale force winds and 4 metre waves were pounding the Baffin Island coast. Once conditions improved, we pulled anchor and headed north. I looked around the ship, which consists of a bridge, small lab the size of an en-suite bathroom, a kitchen/eating area, two tiny cabins and a v-berth designed to sleep six with less floor space than my bathroom. This was the total inside space to be shared with 10 others. In the v-berth, I had the bottom bunk of three on the starboard side, it took a special sort of un-graceful yoga move to get in.

On the 12th of September, Jacob, the local observer, joined the ship, we loaded groceries and headed north. On our way out of Clyde Inlet, Jacob pointed out a passing cliff with three red streaks running down the face. He said that there was an old story about a man, a dog and a bear. All three fell off the edge of the cliff leaving the red streaks, but only the man and bear survived. Occasionally, sled tracks are found behind bear footprints, as though the bear now pulls the man’s sled. I took pictures of the cliff, but the snow obscured the three red streaks.

As expected, it was rough out in Baffin Bay, the large swells tossing the ship about (and spilling vanilla in the galley, giving the ship a pleasant odor of fresh baking). The Nuliajuk is very bouncy and I tend to get sea-sick. To keep a horizon in view, I stayed up on the bridge – which also gave me a nice view of passing icebergs (I’ll write a whole post about the icebergs later).

By midnight we arrived in Scott Inlet to start work in the morning. More to follow…

Getting closer; report from Clyde River

It was snowing when we landed in Iqaluit – just lightly, but it was snowing. Our layover was short and were expecting some critical equipment to be dropped off. Stress levels increased as our departure time approached without our equipment arriving. We were waiting for a centrifuge (not sure what we need that for) and the transmitter for the acoustic releases (absolutely critical for our work). At the last minute the equipment arrived, we handed it off to the airline and hopped on the plane.

As I walked through the gate a sticker was put on my boarding pass that said: “First Air regulations provide that no hotels, meals or transportation will be supplied if you are over or under carried from your destination” and we were told that weather in Clyde River looked bad and we were likely headed to Pond Inlet instead. A few hours into the flight we joked that it would be nice to see Pond Inlet, then the pilot came on and told us were would be landing in Clyde River in a few minutes.

It was snowing harder when we arrived, a snow that has arrived about a month earlier than expected. I hope it doesn’t last. The clouds were low, so I couldn’t see much of the surrounding area. The ground is strewn with massive boulders, no doubt dropped off long ago by a retreating glacier. The airport is a small building with a single common room. We stepped inside and watched our luggage be dumped on the ground in the muddy slush in the parking lot. Fortunately, I pack for that sort of thing. As we went outside to collect our gear, a stranger offered us a lift into town and we accepted.

The one hotel in town is closed for renovations, so we are staying at the Inuit Cultural Centre. When I was called to make a reservation I got the impression I was signing on to stay in a barrack style group accommodation with rows of bunk beds – I was totally wrong. I have a spiffy room to myself with a bathroom (I didn’t expect the luxury of my own bathroom). The centre is only a few years old and absolutely lovely. We arrived a 4pm on a Sunday, and I didn’t know there is no food available at the centre and the Northmart, the only store in town, is closed for the day. Fortunately, another guest took pity on us and gave us chicken noodle soup.

The windows in the common room over look the water (a bay I think). A fuel tanker is at anchor replenishing the town’s fuel supply for the winter. Our research vessel isn’t here yet – we hope it will arrive soon. We don’t have permission yet for our work in Scott Inlet. Monday we meet with the local HTA (hunting and trapping association), the group that can authorize our work, hopefully, they grant us their approval and we can set sail for Scott Inlet.

As a tangent: Since I’ve been just waiting around looking out to the bay (the town is out of sight) I’ve spotted a Raven, a Lapland Longspur and an Iceland Gull.

Where I’m heading…

Might see some of these

I’m heading up north again in a few weeks – I won’t believe I’m actually going until I get on the plane as delays are typical, even expected. Excess ice has already pushed our schedule back and it’s impossible to predict what else might come up before I leave.

This year I’m conducting oceanographic sampling in Scott Inlet, a remote fjord on northern Baffin Island. Two moorings were installed on my behalf last summer (I couldn’t go because I was 8 months pregnant at the time). If luck is with me, I’ll get those moorings back, download the data, then put them back into the water for another year. Additionally, my plan is to take as many CTD casts as I can and help out with the other work that will be going on (fish tagging, acoustic moorings and maybe shark wrestling).

I fly into Clyde River, a small town I’ve never been to. All I know so far about the town is the only guest house is closed for renovations. After a night there, I’ll be getting on a small research vessel. I’ve been on this ship before and learned that it gets quite bouncy in rough weather and I tend to get sea-sick (will pack gravel).

To get to Scott Inlet, we’ll have to skirt the edge of Baffin Bay a place I’ve read a lot about. Baffin Bay is a large body of water bound by Greenland to the east, Baffin Island to the west, Ellesmere Island to the north and Davis Strait to the sound. Obviously, locals have known about this place for as long as they have lived there (since about 500 BC). Wikipedia says that John Davis was the first European there in 1585, but I wonder how far the Vikings got exploring the area as I recently saw a documentary about a potential norse trading post on southern Baffin Island (no idea if the show was presenting a fringe idea or not).

Even though Baffin Bay is choked with ice in winter, European whalers frequented the area early in the age where European powers sent sail boats exploring the Arctic. There’s a large polyna (the North Water Polyna), much further north than I will go, that’s highly productive and home to many marine mammals. Baffin Bay is one possible starting point for the North West Passage and many explorers passed through including Sir John Franklin. Interestingly, a B-52 crashed on the ice in 1968 with its nuclear payload.

A couple hundred km north of Clyde River is Scott Inlet, a narrow fjord filled with large islands which I know little about. This time of year the daily mean temperature is 0 degree Celsius, so it could be quite cold. I’ll have to pull out my fuzzy gloves and wool long johns. I wonder if I’ll see northern lights?

Tilting Isopycnals (the simplified version)

Sunset over Cumberland Sound

One of the things I’m attempting to determine is if the Baffin Island Current*, which passes outside of the mouth of Cumberland Sound, bends into the sound. Last summer, we were able to conduct two rounds of CTD** casts at regular intervals across the sound’s mouth. Unfortunately, I wasn’t actually there as I was too pregnant to be at sea. I doubt I would have fit in the bunk as the ship we used is a particularly cramped research vessel (picture here).

Even though it was cramped, the ship had a hull-mounted current meter. Unfortunately, the instrument wasn’t turned on. No one on board had the knowledge to fiddle with it, so I missed out on that data (that’s the way it goes sometimes). Without measured currents, how does one infer water flow from CTD data?

The Baffin Island Current is geostrophic, that is, the pressure gradient force is balanced by the Coriolis force. In this case, friction and tides become unimportant and can be ignored when calculating current flows.

The pressure gradient force is the weight of water as the sea surface height is not at the same everywhere. This force is always directed from areas with high pressure to areas of low pressure. Without a balancing force, a parcel of water will move from the area of high pressure to the low one. But, there is another force out there to balance with – the Coriolis force.

Actually, the Coriolis force isn’t a real force; instead it is like an imaginary friend that shows up to solve a problem. It pops up when we treat our rotating planet as though it’s an inertial frame of reference to use Newton’s laws. Newton’s laws form the base of ocean physics – and most other things that aren’t moving too fast or are too small. Now, we’ll move on to pretending the Coriolis force is real. This force acts in different directions depending on the hemisphere, since I work in the northern hemisphere, I’ll take it as acting to the right.

As soon as the parcel of water from above starts to move because of the pressure gradient force, it will be acted upon by the Coriolis force and deflected to the right. The result will be a current that flows along an isobar (line of constant pressure) – a geostrophic flow.

In the ocean, pressure is difficult to measure. Fortunately, pressure is related to density and density depends on salinity and temperature which I measured. In the Arctic, where Cumberland Sound is, density depends mostly on the salinity, however, since I measured both I used both. I’ve calculated density and plotted up lines of constant density, which are called isopycnals. From plotting a cross-section of density, isopycnal slopes tell us if water flows in or out of the section, which is exactly what I’m looking for (note: isobars and isopycnals have opposite slopes).

From isopycnal slopes, a relative velocity can be calculated as currents move faster where the isopycnal slopes are steeper. Actual velocities would have been nice to get, leaving me wishing I had been on the ship to turn on the current meter. However, relative velocities still answer my question of whether the Baffin Island Current bends into my site. The answer is yes it does.

*The Baffin Island Current is the official name of this current which passes along the coast of Baffin Island (a nice diagram showing it can be found in this paper). Many currents have assigned names, the Gulf Stream and Kuroshio are perhaps more familiar examples. 

**CTD stands for Conductivity Temperature Depth. From conductivity, salinity is calculated. This instrument samples the water as it descends directly down from the ship resulting in profiles of these properties with depth.

Waves in the Ocean – redone

A photo of waves taken from the safety of the shore

Some time back, I wrote about how, once you are out of sight of the shore, waves in the ocean look the same at different heights (original post is here). I reworked the post, removing the helicopter scariness for the UVic Ocean Student Society’s blog – find the post here.

Something on glass sponges…

Here I am building a mooring

For my masters work I looked at flow over a local glass sponge reef. It turns out that how the tides interact with a sub-surface ridge may influence the conditions the sponge reef lives in. I wrote a little about it for the UVic Ocean Student Society here.