My Hatch and 15 Other Things That Can Hurt You on a Schooner, an Autobiography

Posted on September 9, 2016 by vegathur

Like most of the sailors and science crew, I’m currently covered in bruises and cuts and abrasions. A sail boat is a veritable ER doctor’s dream because literally almost everything on it can hurt you due to the fact that the floor is moving and there is lots of stuff everywhere to fall and slip onto, whack your noggin on, crunch your fingers and toes in, and basically disfigure you continuously. So here is a little summary of the most notable injuries I or others have sustained since I’ve arrived.

1. The Hatch

This mini door that allows fresh air to be exchanged with stank in my room is the bane of my current existence. It hangs down from the middle of my ceiling in my cabin, which is often where my head is also located. I’ve stopped counting now the number of times I’ve hurt myself on this jerk, but I’ve hit basically every part of my head on this thing, the front, back, sides, and even poked my eye on it. F-bombs galore.

2. Doorways

I’m lucky enough that with my height this is less of a problem for me, but every day I see someone whack the front or back of their heads on these. I am more prone to hitting my arms on the sides when a big wave hits.

3. Steps

Toes and feet beware, as there are many of these to stub yourself on. Some are wood and some are metal, but all hurt.

4. Dishes

When this boat is a rocking those dishes and knives can go flying. The trick during meals is to gauge the period and height of those waves and get your mitts ready to grab whatever flies off the table. Yesterday in the middle of the night I got so sick of listening to the dishes smash into the side of their storage space I got up and stuffed the dish towels around them. Surprised this wasn’t standard operating procedure before, although it seems to have been adopted now.

5. The Deck

Actually this was my first introduction to the pain inflicted by the boat. On my first night watch I tripped on a line (see #11) while checking out a strange noise in the dark and wham….the whole left side of my body was strongly caressing the deck of the boat. Ow. But I somehow managed to not hit any of the random metal things on the deck so I think that’s a win-win. Plus it was a good lesson to learn….always be aware of what’s near your feet.

6. Scuba Tanks

These are some of the more scary items on a moving vessel. 20-30 pounds of steel that contain pressurize air waiting to come out. In tall cylinder form, these tanks are not stable and warrant severe caution while managing them. The tank holder set up they have here works on three tanks at a time so if you release one you release them all. That means your toes and feet could get crushed if you don’t mind the other two while working on yours.

7. Other People

Throwing your fellow sailors and colleagues under the bus is looked down on in any good crew, but seriously we all seem to find ourselves hitting or hurting each other, physically and emotionally. For example, Marion is cutting onions at this moment and I can’t see anything as a result. But on the super small dinghy, this is especially rampant. I must have clocked or gotten clocked by someone putting on their gear like 3 times already. I had someone put a tank on my foot, and I managed to elbow Chris in the face.Sorry dude. Also since my French is so bad this is where I tend to get teased. During our dive at the super big swell site, I was on watch for the other divers. Two Taranauts, Nico and Monche were waiting with me when I said “Over there guys.” In a not-so-flattering and highly nasal voice (Do I really sound like that?), both French dudes immediately said “Over thereeeeee guyssss!” and then giggled. Hmmm. Interesting. It’s the fact that they both did it simultaneously that suggested to me that this reply was practiced behind my back late in the night when I was asleep. But it’s all in good fun and I’m thick skinned. Next time I will make it even more annoying and high pitch to add to the fun.

8. A Random Box on the Floor

While labelling the other day, (see last blog) I managed to destroy my shin on a plastic box filled with samples. I then realized that the stupid person who put that box right where my leg goes, was my very own self. Nice.

9. The Bathroom Door

Really the bathroom doors should count as two because you can get hurt on both sides, where it latches and where the hinge is. The doors are always kept closed for a reason but if you are unfortunate enough to try to get in one of these small coffin-sized potty rooms and a big wave hits, you better hope your finger isn’t in the hinge (did this yesterday) or on the latch.

10. The boom

It’s called this for a reason. Keep your head away from it.

11. The lines/ropes

While lines (sailors’ term for ropes) will trip you up easily (see ‘the deck’) they can also do all sorts of other horrible things to your body. They can give you a burn and tear small parts off of your body, as Chris and his toe nail found out a few days ago. Chris was moving his scuba tank to secure it when he managed to clip a rope on the deck and bent that sucker right back and then off. Cue cuss words and squeals about the blood. Definitely the biggest ouch since we got here.

12. The boat as a whole

As I mentioned, she rocks, she rolls and she shudders, especially when in big seas. Yesterday in our 15 foot waves and 35 knot winds she rocked, rolled, and shudder half the science team into their beds. Barf city. I was all good all day until the chef served a delicious pasta with blue cheese sauce that sent me on the vomit comet. No one wants to spew blue cheese, believe me.

Panoramas don’t work too well when the ship’s rocking like crazy…

13. A sponge

This one was unexpected, but Guillaume my cleaning partner managed to throw a soapy sponge straight into my face while attempting to toss it to Monche during cleaning time. Soap + eye = sad Becky, but hysterically laughing French sailors (see #7).

14. Your laptop

Besides the induction of seasickness while reading and writing on this, I managed to somehow pinch my leg skin in between the screen and back of the computer while writing on my lap. What is my deal, really?

15. A pineapple

Before we left for Ducie island, Marion our chef had to go shopping on Easter Island for enough supplies to feed 16 people three 3-course French meals for 20 days. That is a lot of food. So I offered to help put the food away. I hauled, packed, and lifted hundreds of pounds of food across the ship. Mostly I managed, but I did end up damaging one orange, crushed one box on a door way, and slit my right wrist. The culprit of the cut wrist was a freaking stray pineapple. In revenge, Marion immediately cut the bastard up into pieces for fruit salad. But there remains one loose pineapple. I got my eyes on you, Pineapple. Come any closer and it’s piña colada time.

Still having good time, though!

A Day in the Life: Tara Edition

Posted on September 7, 2016 by vegathur

Right now it 5:45pm. We are underway to a new mooring because our last one was too rough. The swell was considerable, I’d say 3 meters, and relentless. We were getting beaten up and stuff on the boat was falling and breaking all over the place. Yet with the transit I have some free time to write this blog.

One question I had been asking myself (and so maybe have you) since I found out I’d be on this ship was what an average day would be like. So here’s my first week’s impression of life on Tara. Overall it’s remarkably busy but oddly relaxed. I never feel too rushed like I often do in the field. I do often feel like I am in people’s way, but I guess that comes with living on a boat with 16 people. Hallways and stairwells can really only hold one person, and I am constantly say “Pardon” or “Excuse moi” to get past people when I am on my tenth trip to the stern to get something I ran out of or forgot. Despite this everyone is generally agreeable and pleasant despite my running around and always being in the way.

A day in the life of a Taranaut

An average day consists of 1) eating, 2) cleaning, 3) diving, 4) sample processing, 5) cleaning, 6) eating, 7) dry lab working, 8) more eating, 9) more cleaning, and 10) sleeping. This is a French boat so the eating part is very important, and amazing. Meals are not to be rushed and they are surprisingly formal given the very relaxed nature of the crew. In fact, I got some tut-tuts and stink eye from the crew for trying to finish putting away the samples during lunchtime. Breakfasts are self-serve (lunch and dinner are served) and usually consist of coffee and tea with bread, jam, butter, fruit, and cereal. The French use bowls for their coffee and dunk their bread, butter, and jam into it. A BOWL OF COFFEE! Yes! It’s like my favorite thing ever, and I don’t understand why we American’s have never picked up this tradition. I mean a BOWL of coffee, people! Also Marion, our chef, makes her own jam and butter. Wowzer. I can’t get enough of her passionfruit spread and feel guilty every time I eat more of it cause I know there is not much. In fact she also brought homemade cheese and honey from France along with many other French products.

Dive time; and yes its winter in Easter Island

After breakfast we clean up the kitchen and then prepare for the dive and coral- and water-sampling. This entails packing our sampling bags of five main things: camera, quadrat, sampling bags, hammer/chisel, and slate with underwater paper for sampling notes. We also get our dive gear ready and don our wetsuits. The water here is unusually cold for Polynesia, so we are wearing a 3mm long john suit under a 3mm hooded top. That’s six mm chest and 3 everywhere else. Despite this everyone is cold. After 1 hour underwater in 20°C water you are pretty darn cold. Then we put out the “dinghy” or zeppelin boats and load them up. On day one, I called the dinghy a “zodiac” but was quickly chastised. Apparently this company who makes these inflatable boats is “zeppelin” not “zodiac” and I was warned not to make the mistake again. Um. Okay?

Scientific Tangent:

Fun fact… rapamycin, the commonly used antibiotic, is named after the place where it was discovered, Rapa Nui! This drug comes from a strain of Streptomyces bacteria previously isolated in the soils of Easter Island where we are sampling now.

The dinghy boats are quite nice and feel really sturdy in the water even though they only have 70 horsepower outboard engines. Once the dinghies are launched and the dive gear loaded by crane, we can climb down the ladder into them. This is an interesting experience every time as Tara’s deck sits about 15 feet above the water. Today the swell was about the same height so it took quite a couple of tries for the captain of the zodiac, I mean zeppelin, to get everyone on board unscathed. Getting out was actually more interesting today.

Captain Sam on the dinghy

These dive boats have one captain and can fit another 7 people on them. We work in teams of three underwater so that’s two teams and one “watcher”: a person (our dive safety officer actually) who floats in the water and looks for the divers. The captain follows the watcher as we cannot anchor these boats, and in these seas we would never even try. Once we are onboard, we head out on our heading to the GPS point. Today that consisted of a rock motu (island) off the west side of the main harbor of Easter Island. So it was … BIG … out, today. I think that is probably the biggest seas I have ever dove in, although I was never worried about my safety in the least. This crew is not phased by 12 foot seas, and they exude so much confidence and are so relaxed that they make you relaxed and confident too. Plus, I knew that once we were under the water we’d be fine. One issue with these boats, however, is space! It’s hard to put on your gear next to the other divers in such a small boat, so we go one-by-one. This is kind of annoying in big seas, cause if we could all go in at the same time that would reduce seasickness and air use, which seems to be my problem this trip. But it’s all good.

On the dives, we hunt for two very different species of corals, Pocillopora and Porites. These two corals are very different. Pocillopora is small (~20cm across) bushy, bumpy, and hard as diamonds. The other, Porites, is massive (we saw one that was 2 meters across and 3 meters tall), pillared, and soft. They also have different reproductive strategies and grow at different rates. Basically they represent very different spectrums of corals, which is why we chose them. At each site we need to collect small samples of 10 colonies of each of these species for the variety of analyses we aim to do (which will be another blog post). This is not a problem at all here because those are the ONLY two species we could find anyways. But in other places, it will be difficult to find them among all the coral diversity. Easter Island, like many remote places, has very few species and 25% of its species are endemic (meaning they exist here). Since this research cruise is to evaluate corals across the Pacific we had to pick two species that are pan-Pacific. Thus another reason we chose those two species for this study.

Diver job: find coral, take sample, photograph coral, fin.

To be as efficient as possible, underwater, each diver has a specific task. One person finds the proper specimen, confirms its taxonomy (easier said than done) and then takes some data about the specimen including taking a photograph of two. A second person cuts small fragments of the coral and puts it into some bags that the third diver is holding along with all the materials divers number one and two might need. This sounds really easy huh? Well today my job was the camera person and I sucked at it, literally and figurative. Personally, I blame the swell.

Now 12 foot seas are fine if you are diving deep but this site wasn’t deep (12-15 meters), and we were close enough to the shore that it was like being in a washing machine underwater. One second you were above your coral and the next you were 30 feet away on the other side of the reef. Wheeeee! I actually think this is kind of fun, like an underwater rollercoaster… but not when you are trying to photograph something or sample it. So we ended up holding onto the substrate as hard as we could and sometimes getting slammed into the rocks around us. Some places were better as the surge was less, but for the most part it was a bit ridiculous and most importantly frustratingly slow for sampling.

Again I want to reiterate that I was never scared or worried that we were in a dangerous situation. It was very safe, just hard sampling conditions. My biggest issue ended up being air. I use a little tank. I’m a shorty and these are steel tanks and super heavy and anything bigger and I’d be unable to swim. These tanks generally only have 200 bar in my tank (or about 2000 psi) when everyone else has 300 to 350. So after fighting the swell for 40 minutes, I was at my limited 50 bar and needed to go do a safety stop and get in the boat. Emilie and Gullaume, my buddies, swam back to the boat with me but still had air so they managed to go back down and finish up without me. So I sucked my air. When we got back to the boat and checked out the photos…. we also realized that somehow I manage to take videos and not photos of the individual corals. So I sucked at taking pictures too. Nice. I am so “that” person right now; the person who runs out of air first and didn’t even do a good job at their job which was pretty darn simple. At least I didn’t get seasick on the boat too which can’t be said for all the divers. And luckily I have a few more dives ahead of me to redeem myself. Lastly, I asked Monche (our dive safety guy) for a bigger tank, so I can suck more air and not worry about it.

Pocillopora

Once back on the boat we have to weigh and count all the pieces of coral to confirm we followed our permit and then process all the samples. Here in Easter Island the authorities actually watched us do this every day. While normally we’d do this the moment we get aboard we have added an additional step to this pipeline here in Easter Island… shower and warm up. With the wetsuits and exertion from fighting the swell no one was really cold at the end of the dive. But add a 40-minute boat ride to that and everyone was cold, really cold. So most of us stripped off of our gear and headed to the showers. After warming up in a three-minute shower (our allotted fresh water for the day) we tackled the samples which takes about 1 hour with six people. Sadly, we won’t have six people at our next two stops so it will take longer.

Porites

4 hour lunch

After sample processing and cleaning up we head to lunch, which is usually consists of very large portions of food including a salad, a grain or pasta, and some vegetable and/or cheese dish like a stuffed pie or stew or curry. There is always a French dessert of cake or pots de cream or fruit and yogurt at the end too. Yum. Oh and more coffee of course. As I said everyone takes time with their lunch which often goes more than an hour. People generally do their daily chores then too, like vacuuming the floor, washing the showers, or the worst job, cleaning the toilets.

After the boat is cleaned we start working on the next aspect of science, LABELING. Labels, labels, labels. Even more labels: Making labels. Sticking labels on tubes. Sticking labels on bags. Sticking labels to sheets. Sticking labels to labels. Lots and lots of labels. Think… four people and 1.5 hours of non-stop labeling. But labeling is somewhat meditative actually, and it’s a skill every scientist should have. That and making stuff out of PVC, duck-tape, and zip ties.

So after all that, it’s around 3 or 4pm and many of us take a nap. I napped on the first day of the dive and it screwed my night sleep up bad I’ve been skipping the nap since. But as you’ll see on the dinner section, napping is important for not falling asleep in one’s European dinner. While people nap, I’ve been reading emails or writing comments on papers or writing a blog, ha. I’ve also been trying to make sure all the science stuff is cleaned up. It’s easy to leave stuff around and sailors don’t like things lying around. Also the dive gear needs to be cleaned and put away. Our dive safety office often does this while we process the samples, but there is always more to do.

Taranaut Pascal

European dinner… late.

While we were processing samples and labeling, the other dive team was out collecting plankton and doing the benthic transect videos. Given the lateness of these dives that team often isn’t done with stuff and back on the boat until around 5. Then people are basically finishing cleaning up and the crew get everything ready for the evening around 7. Since they are French, dinner often doesn’t start until 9pm. Plus, while the food is served no one touches it till everyone is sitting down which can sometimes take quite a while because the crew is in charge of a lot of things. Dinner is again three courses and people chat often until 10:30. If you are on dishes that means you are washing and drying till 11pm. The night watch starts at 11pm but most of the crew stay up for another hour or so. So it’s a long day but a good day.

Rock me mama, like a wagon wheel – or like an 83-foot schooner.

Even though she can rock pretty hard, sleeping is not hard here, at least not for me. In fact, I rather like the swaying; it feels like being rocked to sleep, and it’s even sometimes hard to not get sleepy from the constant rocking when you are just sitting around. Also my bunk bed is quite large and comfortable. I did, however, get the short end of the cabin stick. My room is the one closest to the galley so it’s a tad loud. But that’s not too bad. The main issue is that it’s also unfortunately above the gas and bilge. Think stinky. Super stinky. Stinky enough that I have to cover my face and even gag sometimes. Each night I turn on my fan, open my hatch, and open my door to get the fumes to dissipate enough that I don’t get brain damage from sniffing gas. If we’re moving I can’t have the hatch open and therefore I try to stay out of the room. I’ve spoken with the crew and they are aware that it’s the stinky room but someone has to sleep in it ‘cause there is not enough room on the boat otherwise, every bunk is taken. Hopefully I can convince the captain that this is a minor form of torture and that I should get to switch to a new room after a week or so. For now, I will keep my complaints to myself and suffer the stank in silence.

Have sweatshirt will travel

Posted on September 5, 2016 by vegathur

So what does one need to pack for a 5-week scientific trip, 4 of which are on a sail boat? Clearly I couldn’t bring everything I would have liked. Also much of the dive gear I would need is provided (regulator and BC) as are the materials for sampling and storing the coral samples were to collect. But still, in packing for Tara, I was highly concerned about space, so I devised a plan under the assumption that I would have no access to civilization for 4 weeks… oh wait that’s true. So here is a list of my gear and comments on many of them. Noticeably lacking is a rain jacket (face palm), but thus far I think I this was a good standard list and would have been even appropriate for a longer trip.

Electronics

Can’t really travel these days without a ridiculous assortment of things that can get fried in seawater and are really expensive. I tried to limit mine to just a few but it kept adding up so in the end it’s just 10 things. Had this been my husband’s blog it would be considerably more, so I am feeling smug.

Laptop with charger. Ahh my lemon Mac lap. Clearly I had to bring it but this POS has windows office crash relatively commonly and its key board loves to stop working for no reason…see spare mouse. Had to buy this POS last year when we were in Curacao and mine was stolen by some a****** who broke into our house and took all the electronics and my wallet from the main room.
Hard drive for backing up all my stuff from Tara and that includes all my stuff from my desktop back home sans my Next Gen Sequencing libraries. So I can work and complete all those papers and revisions that are outstanding….yeah time to work on papers!
iPad for reading in bed mostly, with many recently-acquired YA books about various kinds of magicians and mythical creatures! Downside…doesn’t help with finishing those manuscripts.
iPhone which apparently now is just an expensive paper weight in my gear cause I have no service. Will be important again when I return to the US I guess.
Two USA-to-Euro converters ’cause why pack one when two are better?
Noise cancelling headphones with extra batteries and cords for engine noise and French lessons. C’est bon!
Dive watch with the necessary instructional manual because last time I dove in Hawaii all it said was “wet” the whole time and didn’t record a single dive. To the company who made that computer…really?…really really?.. why is that even a setting?
Headlamp for walking around at night. Shit’s dark in the middle of nowhere.
Spare mouse for crappy laptop (see number 1).
Digital camera. An oldie but a goodie. Ended up donating my flash card to the Tara underwater cameras so currently is useless. Hello iPhone.

Luggage and Gear

Like any good expedition, this trip was a great excuse to buy even more kit and gear to take up space and collect dust in my garage and lab for 11 months of the year. For example, item #one was an item I have wanted for many years, but had no reason to plop down the $140 (actually $98 thank you end-of-the-summer sale) in cash for. But hey…I’m on a boat so any gear needs to be water proof and relatively small right?, so cha-ching!

One super hot and stylish 45 liter ‘Bottomless Pit’ duffle bag from Patagonia (cue hand wringing). Fully water proof! Shoulder backpack straps for easy carrying through airports! Sea blue and oh so shiny! Got a crap ton of stuff in it, including my full size fins, people. Its name ran true as it did seem bottomless.
Timbuktu personally designed laptop case. Had one of these given to me in 2005 by my father in law. It never died and was still is in amazing shape after spending some time at the bottom of the sea (whoops) and in a cooler filled with fish (double whoops). So this last year I got a new one that I designed myself. Note to future buyers, go with the Velcro covers…my clothes and my couch are destroyed.
Mask, fins, booties, and gardening gloves for diving. While most the gear is provided, I’m just not comfortable diving without these very personal items. I like to know that I won’t have a leaky and foggy mask or weak-ass fins that are gonna give me leg cramps or worse fall off in any current.
3mm Scuba Pro wetsuit. Had to get a new one after 7 years of wearing the other one and constantly complaining that I needed a new one cause mine was jacked from hundreds of hours underwater. Now I can’t complain about it, right Ryan and Deron?
Two pairs sunnies (sunglasses, mate), croakies (to keep said glasses on neck or afloat), and a case to store them in the event I throw something on them or have my bag unceremoniously thrown on the boat.
1 pair eye glasses that if they break I’m screwed.
Mechanical pencils and sharpies (required science gear).
Blue nitrile gloves (see above parenthetical statement).
Hair brush and many hair ties to lose in the ocean (ladies and dudes with man buns you know what I am talking about).
As Zapphoid recommends, 1 towel to dry oneself and double as a blanket and other things (see Hitchhikers Guide to the Galaxy).

Eating dinner with the crew

Toiletries

Sunscreen for keeping the cancer at bay.
Hippie biodegradable toothpaste for keeping the bad breath and cavities at bay…tastes horrible.
Face lotion, which I probably won’t use till Moorea.
Lip balm.
A thousand kinds of decongestant and anti-diarrhea meds cause well…the tropics…see section on viral diseases below.
Body lotion, which in retrospect is likely unnecessary given the humidity.

Clothes

5 pairs Patagonia travel chonies (underpants, gringos) which are washable and easily dried. Don’t travel without these ladies.
3 swim suits, two of which are Patagonia-made and they should sponsor me ’cause I buy all their stuff and even though the stuff’s expensive it’s really worth it. I buy the same damn swim suit every field season and it rocks for serious underwater work. No messy or uncomfortable straps and can take my hard wear and tear.
5 t-shirts (probably too many).
3 tank tops (ditto).
3 pairs of shorts: 1 nice, 1 water use, 1 for daily wear.
2 pants: 1 nice for meeting with important people, 1 for cool nights and morning.
1 pair of tights. I found that traveling in these is very comfortable, warm, and easy.
1 skirt for fancy night and attempting to look respectful…probably failing.
2 long-sleeved technical fabric shirts for cool nights and bug repellent.
1 Patagonia R-1 technical fleece jacket. Have worn everyday since I got here.
1 old manky Stanford sweatshirt. Can’t go anywhere without this baby, even though its older than most of you reading this blog. My dad bought it for me in 1998 when I got into Stanford for graduate school. It’s like my safety blanket and has been to every continent sans Antarctica with me. Many photos of me in the field show me in this POS. It’s ripped to shreds at the cuffs and is not warm at all anymore, but it does serve as a shield from the tropical cold after a dive and keeps the mossies (mosquitos, people), sand flies, and other nasties that want a piece of me from getting a bite.

Moai and Tara

Scientific tangent: Zika virus

Since I am a scientist that studies viruses, perhaps this blog should have something useful in it. So here’s an educational tangent, about Zika. Zika virus is one of the diseases that I aim to prevent by wearing long shirts and pants while working in the tropics. I’ve already got a few tropical diseases (amoebic dysentery being the most recent and wow did that suck) but for the most part have been lucky. Yet many researchers who travel to and of course the people who live in the areas we work are exposed to many serious tropical viral diseases, the most currently notorious of which is Zika virus. Zika is an arbovirus in the viral family Flaviviridae that includes Dengue and West Nile.

Zika virus was originally discovered in African monkeys in the 1940’s by people looking for Yellow Fever. Although all the most recent discussions of Zika have focused on Brazil, and although the origin of the disease is Africa in where there were small outbreaks since the 1950’s, the first major Zika outbreak was on the island of Yap in the South Pacific in the late 1990’s where it infected a large majority of the inhabitants. Since I don’t have access to the internet I can’t give you any numbers; clearly I’ve become too dependent on Wikipedia. But this major outbreak outside of Africa was probably due to transmission of the virus from its native African mosquito (Aedes egypti) to other more urban-style and broadly prevalent mosquitos like Aedes albopictus.

But the second outbreak was in Moorea, the French Polynesian island that Tara will land at in October and where my lab’s recent research on coral reef viruses and bacteria is focused. When the outbreak occurred in Moorea, it was first thought to be a nasty strain of dengue fever or West Nile, two other mosquito borne viral diseases with the similar symptoms of high fever, rash, and severe nerve and joint pain. Again, like on Yap, a large portion of the population got the disease in Moorea, and it was severe enough that people sought treatment at the local hospital, which was overwhelmed. It wasn’t until the 2015 Brazilian outbreak that people realized in retrospect that the outbreak in Moorea was not dengue.

Effects and Treatment of Zika

Two major complications of this nasty disease are birth defects and neurological issues that are long-lasting. One of the researchers I met in Moorea had been afflicted with the virus in 2009 (I think) and she still suffers from partial paralysis in her left leg. My cousin in Dominican Republic got a similar symptom from West Nile. This is symptom is called Guillain-Barré (French pronunciation) disease and includes a variety of neurological signs and symptoms. For those who are curious, a sign of a disease is something that is visual like a rash, but a symptom is something that is recorded like fatigue or malaise. Anyways, remember, at the time of the Moorea outbreak, Zika was not rediscovered yet and so data were not taken on the number of children and adults or their signs and symptoms that were associated with this outbreak. But just last year, however, the World Health Organization started using the local doctors on French Polynesia to determine if the outbreak then also caused an outbreak of microcephaly in Moorea and Yap as it has been shown in Brazil. Since the population of these small Polynesian islands is very low, the doctors generally know almost all the local residents, so this kind of work can be done. To my knowledge it is unclear what the results of these outbreaks were in those two islands, but based on the 4 different and very large signs I saw at the Easter Island airport, it’s very clear people are concerned here. And they should be, as this new disease can be very serious to adults and pregnant mothers. Scientist have also found that it can be transmitted in bodily fluids such as blood and also sexually transmitted. Research on Zika has been very fast paced, and just recently a receptor that is unique to the virus was discovered, so hopefully we’ll have a vaccine soon. At the same time, methods to prevent spread of the virus have been using symbiotic bacteria that infect the mosquitos has not only been developed but actually used in urban areas in USA. However, taking personal protections to prevent breeding of and bites from mossies are the most essential way to keep Zika at bay.

Day 1 on the Tara

Posted on September 2, 2016 by vegathur

Tally:

22 hours of travel: one car, three planes, one taxi, one hike, one boat trip.

4 whacks to the head on my hatch.

1 face plant on the deck.

1 beer.

At least 10 cups of coffee.

1 amazing fish stew.

Getting there

So here I am, on the Tara Expedition. When I started this blog it was 7pm last night and the crew was returning from some much needed shore leave and exercise. They have been at sea for two weeks straight so it’s not surprising they want to stretch their legs. The flights here were mostly easy – many, but easy. My first flight was PDX-Dallas, and we were delayed, leaving me only minutes to pee and buy food before boarding onto the new flight to Santiago. That flight was long but a redeye, so I got at least 4 hours of sleep and got to watch two Marvel movies. Um the X-men movie kind of sucked. How is that even possible?

Bad movies about mutants aside, Chile was a brief but pleasant stop over. I’ve been to Chile before on holiday with Andrew when we toured the southern Torres del Paine National Park and volcano district. Even the two-hour layover reminded how nice and laid back the Chilean people were. The airport was lovely and easy to navigate even with my super crappy Spanish. I longed to spend more time in Chile but that will have to wait till another day.

The flight to Easter Island was surprisingly long – almost six hours; a good reminder how remote this place it. The flight was also remarkably rough. I’ve crossed the Pacific numerous times, and each time there is some turbulence, but that had to be the most intense and sustained turbulence I’ve experienced in a long time. It actually got a bit frightening at one point but the calm of the flight attendants made it seem pretty standard.

Once we arrived into Easter Island / Isla de Pascua / Rapa Nui, I met up with another Taranaut Calixte from Brittany, France, who will be working on the plankton side of the work. He is a young plankton researcher who will be doing a bulk of the water filtering with Guillaume B (there are two Taranauts named Guillaume). One of Tara’s main missions is to catalogue the various plankton communities across the sea. Guillaume told me they have already sampled over 60 sites on his watch. We waited for Calixte’s bag in vain, as his connection was so close from Miami to Santiago that his luggage did not make it. Neither did Chris Voolstra, another Tara PI and our collaborator from the Red Sea, who was delayed overnight in Frankfurt due to a whole airport shutting down due to a security breach. But we were given the bags of two other Tara folk who missed their luggage earlier in the week, so it was win win.

A Polynesian island like no other

Landing in Easter Island, I was immediately struck how different it is than the rest of Polynesia. It is not tall like the Hawaiian Islands or Tahiti or Moorea. It is rather flat with oddly short and squat cinder cones of the volcanos jutting out at the corners. Also, hearing Spanish being spoken in Polynesia is rather disarming, albeit comforting for this non-French speaker. Polynesia’s sordid history is clearly displayed when you realize that in all the islands there are many different languages spoken: English in the Hawaiian Islands, Samoa and New Zealand, French in the Southern French Islands, and Spanish here. The history of this island is strange, mysterious, and also rife with the colonial conquest issues of the past. Chile acquired Easter Island in the late 1880’s but not before many of the locals were either killed or expatriated. It was even run by Mooreans at some point, and also offered up to the British who oddly passed. Unfortunately, we didn’t have time to see any of the Moai statues for which Easter Island is famous, but we we will be here a few more days and hopefully get off the boat to see some of the sites.

Onboard Tara

To get to the boat we hired a cab, and when we told him where we were he had never heard of it but figured it out from our description. Also, I had seen Tara from the air so we knew where she was moored. We had to walk our luggage down a steep ravine but it was pleasant outside and another boat was moored alongside Tara. The crew of that ship was at the dock and agreed to buzz our boat and let them know we were waiting ashore. We got picked up at the same time as many of the crew were leaving to spend the afternoon in town. I quickly and sheepishly said hello and gave the required 2-cheek kisses. But then we were rushed off to the boat.

Once on board I wasn’t sure what to do with myself (I still don’t, which is why I am writing this). I image I will feel like for some time until I get my bearings and some directed science tasks. I did meet the captain, Sam, and keeper of the house Marion, immediately. Marion showed me my room, and I hastily unpacked my seasick meds and took 2 before I could succumb. My room is quite sizable and my decision to pack lightly was unnecessary really as there is quite a bit of free storage space.

The boat is really large but the seas here are quite rough, and so we are rocking pretty good. I hung out with another scientist, Emilie Boisson, on the back deck for a few hours, and we talked about the project and some logistics while occasionally laying down on the sea pads to feel better (she was slightly sea sick, too). The air is quite cool and that is nice. I was evening wearing my sweater and pants to stay warm most of the night.

After a while I realized how tired I was (only got about 5 hours of sleep and in a plane, so not good sleep), and so I took a short 1-hour nap. I felt remarkably well after that and even began this blog in the cabin without getting seasick (knock on wood). Dinner was started by Marion and Sam and when I asked if I could help they told me to start drinking beers. Now that’s a task I can do. Dinner was served quite late, around 8 (how European), and really excellent, ling cod (I think based on her description of the fish and its taste and texture) and vegetable curry stew with brown rice and salad. I ate just a little for fear of getting sick (no one wants to barf curry, much alone fish curry), but I wanted like three humongous plates of that stew. I hope all the meals are as amazing.

After dinner I was briefed on some of my duties. As all members of the crew, I am responsible for lunch and dinner duties as well as night watch. Tasks for meals include service (setting the table and serving people), dishes (self-explanatory), and cleaning up. ‘Watch’ is an hour long duty everyone does each night. This essential job requires that you scan the instruments for issues like coming off our safe mooring site (not good), the dinghies or lines on the deck getting screwed up (bad), water in the instruments (very bad), and fire (really really bad). If any of these things happen then I relinquish any responsibility to someone else. For example, if our boat comes off its anchor or drifts too far into a danger zone I wake up Nico, who by my understanding is the second in command. If the wind speeds get above 25 knots (it was around 17-21 during my watch) then I wake up Nico. If there are any water or fire alarms, then I… you guessed it… wake up Nico. The only thing I can do on my own is close the hatches if it begins to rain. All in all, not a bad job, and the hour went quickly, but thank god I took that nap ‘cause I was pretty knackered. I got an early watch, so luckily I could sleep all night after 11pm. I think that was pretty kind of them. In retrospect, I wish I had brought my sweatshirt to watch and also peed beforehand. The only incident during my watch was me eating it on the deck when I tripped over a line while I was checking out a strange noise which ended up being two crew fixing something at the bow. I guess it was a good early lesson to learn… always look at where you are stepping on the deck cause there is a ton of things on it to make you fall down.

Becky’s on the Tara Expedition: Coral Viruses Across the Pacific

Posted on August 23, 2016 by vegathur

The Tara Trip

Apprehension. Excitement. Honor. Complete terror and insane wonder. These are the feelings I have been going through (sometimes all in the same five minutes) when I think about my voyage on the Tara. Tara you say? Yes Tara! Tara is a 36 meter (that’s ~110 ft for you Americans) sailing ship, devoted to the collection scientific samples and the dissemination of knowledge and good will across the world. Tara is currently on its 11^th oceanic mission called the Tara Pacific Expedition which our lab was asked to join back in late 2015. Our lab’s mission is to help collect, catalogue and evaluate the viruses associated with two species of coral across the entire Pacific. In December of 2015 I travelled to Tara headquarters in Paris with my postdoctoral research and colleague Dr. Jerome Payet, who is an expert in aquatic virus ecology and conveniently French. Jerome helped me navigate and fall in love with Paris those few days (merci beaucoup Jerome!) but more importantly helped the newly assembled Tara Pacific Team devise a sampling strategy and determine a few of the many logistical issues associated with the coral virus aspects of this expedition.

Tara anchored in Panama during the first leg of the trip. Photo by Maren Ziegler.

Most of the members of the scientific and logistics team are European (mostly French), as the Tara program is funded by the European Union and other European and international partners. In fact, our lab is only one of two non-European labs heading the scientific mission of the Tara Pacific expedition, and on the boat I will be the only one who doesn’t speak French. Doh! But what an honor to be chosen to lead this endeavor, and we were so lucky to be asked to participate! Thanks to everyone who threw our names into the collaborator hat!

Becky and ‘conveniently French’ Jerome during the planning meeting in Paris.

The Tara Team

So since December the Tara team has been tirelessly getting the boat, equipment, permits, and all the amazing amount of paperwork and other 10,000 things done to launch the expedition in May. The boat successfully sailed from Paris to Miami and then Miami through the Panama Canal where the first leg of this year’s expedition started. Our very own Ryan McMinds was sent on that leg where he was instrumental in augmenting and finalizing the underwater protocol for collecting the corals. Ryan along with our friend and collaborator from KAUST Maren and ended their trips on the west coast of Panama.

Collection site in Panama. Photo by Ryan McMinds

Can You Say Remote?

Currently the sailing team is in route to Easter Island (Rapa Nui) where I will meet them and journey across some of the most remote islands in the world. And therein lays my apprehension and terror. Now I’ve travelled a lot to many remote and foreign places. I have spent hours and hours on small boats doing coastal marine science, and I have logged hundreds of hours of dive time underwater in many tropical locations. But I have never spent more than 7 days on a boat, and that boat was an 83m (273ft) research vessel Atlantis, not a sail boat! Many of you might think I’m pretty adventurous, but I’m going to admit that I am kind of a wuss. I love traveling in retrospect, but usually when I do it I just want to go home. Yet I need to do this. It’s something every marine biologist dreams of…to be cliché…it’s a once in a lifetime opportunity. Expeditions like these are amazing life experiences both personally and career wise. It’s gonna forge new scientific collaborations and probably generate life-long bonds among the science team and crew. Never the less my ulcers get a little bigger each time I think about being at sea in the middle of nowhere. Well… it’s not that far you say? Oh yeah? So Easter Island/Rapa Nui is 2,182 miles from its protectorate nation of Chile. Its closest neighbor island is the least populous (only 56 people live there) nation in the world, Pitcairn which is famous for its descendants of the mutinous Bounty crew, a short 1,289 miles away. The island where we disembark, Gambier/Mangareva, is a short jaunt of 1,619 miles away. Also I will have no internet (yeah no politics for 4 weeks) or email (I dread my inbox on the day I return)! YES MIDDLE OF NO WHERE!

Famous Moai on Easter Island. Photo from Wikipedia.

Can You Say, Pristine?

Fortunately middle of nowhere might also mean some of the most pristine reefs of the world. I can barely imagine what I will see and experience. Whales? Sharks? Whale sharks (please please please)? Coral cover and species diversity like I’ve never seen? I hope. I’m also super excited about the microbiology we will be uncovering. We’ve never done such an extensive latitudinal and longitudinal survey of the microbes and viruses associated with corals before. This Tara trip will likely uncover new taxa and diversity like we’ve never recorded before. We might also be able to say what drives much of the co-evolution of these taxa with their symbionts. The data will be a long way in coming, but combining our GCMP data, we’ll hopefully have the most extensive geographical and phylogenetic analysis of the coral holobiont in history thus far. So I’ll keep you updated on the adventure. Wish me good weather, scientific luck, and whale sharks. Au revoir!

Hoping this Panamanian shark’s cousins come out to play in the South Pacific. Photo by Ryan McMinds.

What does a marine biologist do in a landlocked country? Study elephants…

Posted on March 20, 2016 by rosaless

On my first post I declared that I would write about marine mammals, but things have changed since then and now I hope you also welcome posts about the microbiology of elephants. To make the transition easier I will show you a picture of a baby elephant.

Baby Asian elephant at the Elephant Breeding Center in Chitwan

Why I am studying elephants?

I was lucky enough to be given an NSF GRIP award. The goal of GRIP is to partner students with federal agencies. A great opportunity for me since one of my goals has been to work at the Smithsonian. I looked for researchers at the Smithsonian that were taking GRIP students and working with viruses. The lab that peaked my interest was at the Smithsonian National Zoo and works on elephant endotheliotrophic herpes virus (EEHV), a herpesvirus that was detected as fatal only in 1995. Since then about eight different types of EEHV have been detected, but EEHV1 is the most pathogenic. This virus is specifically deleterious to young elephants and can progress to death within 1-7 days after symptoms arise. It has mostly been found in Asian elephants, but there have been some accounts of EEHV African elephant infections.

The project

My project sounded pretty amazing. I would go to the Smithsonian to get some molecular biology training and then fly to Nepal, live for 4 weeks in Chitwan National Park, and check elephants for EEHV; thus saving the baby elephants!!! To sample elephants I will take trunk wash samples since its one of the most effective ways to test elephants for this virus. Basically, a veterinarian pours some saline (salt and water) down an elephants trunk and the mahout instructs the elephant to blow it back out into a container.

Reality

After a two week training at the Smithsonian, I packed up my molecular and fieldwork bags and landed in Kathmandu, Nepal. My plan was to collect samples the week I landed. Two and half weeks later and I just collected my first set of trunk wash samples. I declared them the most beautiful thing I’ve seen in Nepal. Not that Nepal is not a beautiful country (e.g. picture below), just that the hurdles to get these trunk washes illuminated my tubes of samples with a magical essence.

Rhino making its way to the Rapti river in Chitwan

The struggle

In addition to working with the Smithsonian, I also wanted to develop my fieldwork skills. So why not attempt fieldwork on a topic I just learned, on field techniques I am not trained to do, in a country where I don’t speak the language, and where electricity is sparse. Needless to say many problems occurred, from permits, to miscommunication about the support available to me in the field, and socioeconomic problems.

While I have been able to manage many of the problems because of the help of local Chitwan people and the support from NTNC, the socioeconomic aspect of this experience has been the most difficult and thought provoking. I think I used the word “socioeconomic” in almost all the proposals I wrote on this project, but I had a limited understanding on how my project could affect the economy or society in Chitwan’s elephant industry. I thought my research would provide a free healthcare service to the elephants of Nepal and people would be mostly enthusiastic about my study, right? Wrong.

I was advised to work with elephants that are privately owned, which are mostly used for tourism. While I have not spoken with all the owners, I have talked to some of the major members in the committee and the consensus from the ~45 elephant owners has been that my study would be a burden to them both economically and socially. Why do they think this, you ask? Their hesitance comes from a previous study conducted to survey elephants with Tuberculosis (TB). A bacterial disease that infects many mammals including humans and elephants and is transmitted through the air.

I was told that elephants that were diagnosed with TB could no longer partake in tourist activities (to avoid transmitting TB to people) and were not allowed into the forest (to avoid transmitting TB to the wildlife) until the elephants were treated for TB. Now it is seen as an economically poor decision to have scientist look for a pathogen in their elephants, because they risk losing money from tourism and are forced to treat their elephants. These consequences were especially troubling, because besides the diagnosis their animals looked otherwise healthy. Also, a positively diagnosed animal may be seen in the community as inferior and may decrease the animal’s value.

My solution

The elephant owners protested that if a diagnosis of an illness is made then the scientist must also provide a solution and treatment. However, I can not provide these resources. Instead I tried to provide education about EEHV to elephant owners. For instance, TB is not like EEHV and should not affect the owners economically. EEHV has not been shown to be transmissible to humans or other animals, so tourism should not be affected. If an adult elephant was diagnosed with EEHV they do not need to be treated, but it is important to know that they can transfer the virus to a calf.

Although, mostly (and I mean mostly) all the elephant owners are skeptical about my research there was enough of them that supported my study; hence the picture of my beautiful sample collection.

Elephant trunk wash samples.

Ever wonder what’s inside of the brain of a harbor seal?

Posted on December 20, 2015 by rosaless

As promised I am here to provide some new information about marine mammals. I know you’ve waited too long. This time I will be telling you about my very own research that was just published in PLOS ONE!!! This is my first, first author publication so there was a steep learning curve on data analysis, graphing, and the publication process. In future post I plan on taking the reader on the journey of my first publication. Especially the struggles, since the public often doesn’t hear about that side of science.

For this blog I will give a quick synopsis of my paper for those who just really want to know what I found inside the brains of Pacific harbor seals. Although, before I get to the nitty gritty of my story I like to tell you a bit about my study subjects, the harbor seals. I mostly worked with pups (< 1 month) and weaned (1 -12 months) harbor seals, which tend to be born between February and April. Their mothers wean them for about 3-4 weeks and soon after they begin to catch small fish and shrimp. During these early stages of life, they encounter many dangerous situations for example, being preyed, starvation, and disease.

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Popeye a Pacific harbor seal not related to this study. Photo by me

I am particularly interested in the diseases of young harbor seals, since understanding this may increase their survival rates during this fragile stage of their lives. About 44% of marine mammal diseases remain a mystery. That means that many harbor seals die and we have no idea what’s killing them. So, I wanted to help discover possible culprits that cause marine mammal diseases.

I started my search with the brain tissue of 14 harbor seals that were found sick on the California coast. I first looked into the viral world and I found viruses in four of the animals from the family Herpesviridae, which have previously been found in harbor seal brains in European and North American waters. A virus from this family (Phocine herpesvirus-1, PhV-1) are particularly harmful for young seals since they have an undeveloped immune system.

However, the bacteria side of the story proved to be a bit more interesting. One of our significant discoveries was the presence of Burkholderia along with a high amount of Burkholderia genes that are known to cause disease. Burkholderia is an interesting genus of bacteria that can be zoonotic (passed from animals to humans), but it is also ubiquitous and can be harmless. While this is not the first time someone has looked for bacteria in the brains of marine mammals and found Burkholderia, it is the first time that this bacteria was found in harbor seals in the USA. So where else were Burkholderia found in the brains of marine mammals? Well in Southeast Asia, this bacteria was found in an aquarium, which caused the death of marine mammals.

Our other interesting finding on bacteria comes from Coxiella burnetii. Similar to Burkholderia, it was found at a high abundance with high amounts of disease causing genes. Unlike, Burkholderia it was not found in all our harbor seals, but only in three of our animals. Meaning this pathogen may be less common in harbor seal populations compared to Burkholderia.

C. burnetii is a known pathogen that needs to replicate within a cell (obligate intracellular pathogen). It is best known for causing Q fever, but in marine mammals it causes inflammation of the placenta (placentitis) and it has never been found in the brain of harbor seals. We think since these harbor seals were young animals, the placenta may be a source of C. burnetii infection for pups, but this is just a hypothesis that needs some testing!

So what exactly did we learn from all this? Well our study adds to our knowledge about the distribution of Burkholderia in marine mammals and like in Southeast Asia it may also be causing the death of harbor seals in the USA. Also, now we know that C.burnetii can infect the brains of harbor seals and we should investigate the source of this infection. Finally, we can now begin to monitor for these bacteria in the brains of these animals as possible sources of infections.

Lab Accomplishments: Aliens, Predators, and Brains

Posted on December 17, 2015 by Ryan

I’m a little tardy in writing this, but our lab has a few pieces of stellar news from the last couple of weeks. First off, the most exciting:

Photo from Stephanie Rosales

Meet the man formerly known as Mr. Rory Welsh. He will now be referred to as Dr. Rory Welsh. Or, more likely, still just Rory. This guy is one of the most humble and most awesome guys around. Since he successfully defended his PhD dissertation last week, he is now also formally recognized as an expert in our field, and the foremost expert in his particular corner of it. I know I speak for our whole lab and many others when I say congratulations – you deserve it.

In the course of our tenure as PhD students, we must take classes, teach classes, perform research, and share that research through a number of public presentations. And, most importantly, we must make some verifiable contribution to the collective knowledge of our field. Which brings me to the other fun lab news. During Rory’s dissertation defense preparation, he wrapped up a couple of projects and wrote multiple papers. One was accepted to the influential ISME Journal and became available online just before his defense. Another (which was co-authored by a certain blogging scientist we all know…), he recently submitted to the open-access journal PeerJ and is undergoing the review process. Though it hasn’t yet been accepted, the pre-print also became available online last week. Both of these papers deal with the fascinating ecology of a particular coral-associated bacterial predator called Halobacteriovorax. I could tell you more about it, but I think it’d be best to hear that story straight from the Doctor’s mouth. Rory will tell you about them, soon!

Last week also saw the publication of yet another paper from the lab! Stephanie, who has previously written a post for the blog, had her paper published on the metagenomics of seal brains! It’s available now at another open-access journal, PLOS ONE. Stephanie is also working on a blog post talking about that paper.

Whew! The rest of the lab’s been quite prolific. I definitely feel like I need to step up my game…

Mapmaking: Part 3

Posted on December 12, 2015 by Ryan

In the first two parts of this series, I introduced Lightroom, the Lightroom plugins LR/Transporter and FTP Publisher, and the programming languages AWK and R. With those tools, I organized my photos and got some of their metadata into a format that I can easily manipulate with R code.

After getting the photo information organized, I had a few more pieces of metadata to get together. In particular, I wanted to organize the map based on the taxonomy of the corals, and I wanted to include some information about the site of collection that wasn’t included in my sample metadata file. We are keeping this information in separate files, for a couple of reasons. Over the course of the project, multiple people have collected replicates of the same species of coral in different locations. Every time we collect a coral, we need to fill in a line of data in the sample metadata table. Right now, we have 57 columns in that table, meaning we have to manually fill in 57 pieces of information for each sample. On a whirlwind trip where we collect 50 samples, that adds up quickly to 2850 values, or 2850 opportunities to make a typo or some other error.

If any two columns in our table are highly repetitive and are dependent on each other, we should be able to allow the computer to fill one in based on the other. For example, we could create seven columns in the sample metadata file that detail each sample’s species, genus, family, order, phylogenetic clade, NCBI taxonomy ID number, and perhaps some published physiological data. However, all of these pieces of information are dependent on the first value: the species of coral sampled. If we collect the same species, say, Porites lobata, 25 times throughout the project, all the information associated with that species is going to be repeated again and again in our metadata sheet. However, if instead we create a single column in our sample metadata table for the species ID, we can then create a separate table for all the other information, with only one row per species. We cut down on the amount of manual data entry we have to do by 144 values for that species alone!* Not only does that save time; it helps to avoid errors. The same general principle applies to each site we’ve visited: certain values are consistent and prone to repetition and error, such as various scales of geographical information, measurements of water temperature and visibility, and locally relevant collaborators. So we created another table for ‘sites’. **

Excerpt from 'species' metadata table

genus_species	genus	species	family	clade	TAXON_ID	NCBI_blast_name
Tubastrea coccinea	Tubastrea	coccinea	Dendrophyllidae	II	46700	stony corals
Turbinaria reniformis	Turbinaria	reniformis	Dendrophyllidae	II	1381352	stony corals
Porites astreoides	Porites	astreoides	Poritidae	III	104758	stony corals
Acropora palmata	Acropora	palmata	Acroporidae	VI	6131	stony corals
Pavona maldivensis	Pavona	maldivensis	Agaricidae	VII	1387077	stony corals
Herpolitha limax	Herpolitha	limax	Fungiidae	XI	371667	stony corals
Diploastrea heliopora	Diploastrea	heliopora	Diploastreidae	XV	214969	stony corals
Symphyllia erythraea	Symphyllia	erythraea	Lobophyllidae	XIX	1328287	stony corals
Heliopora coerulea	Heliopora	coerulea	Helioporaceae	Outgroup	86515	blue corals
Stylaster roseous	Stylaster	roseous	Stylasteridae	Outgroup	520406	stony corals

Excerpt from 'sites' metadata table

reef_name	date	reef_type	site_name	country	collected_by	relevant_collaborators	visibility
Big Vickie	20140728	Midshelf inshore reef	Lizard Island	Australia	Ryan McMinds	David Bourne, Katia Nicolet, Kathy Morrow, and many others at JCU, AIMS, and LIRS	12
Horseshoe	20140731	Midshelf inshore reef	Lizard Island	Australia	Ryan McMinds	David Bourne, Katia Nicolet, Kathy Morrow, and many others at JCU, AIMS, and LIRS	15
Al Fahal	20150311	Offshore reef	KAUST House Reefs	Saudi Arabia	Ryan McMinds, Jesse Zaneveld	Chris Voolstra, Maren Ziegler, Anna Roik, and many others at KAUST	Unknown
Far Flats	20150630	Fringing Reef	Lord Howe Island	Australia	Joe Pollock		15
Raffles Lighthouse	20150723	Inshore Reef	Singapore	Singapore	Jesse Zaneveld, Monica Medina	Danwei Huang	4.5
Trou d'Eau	20150817	Lagoon Patch Reef	Reunion West	France	Ryan McMinds, Amelia Foster, Jerome Payet	Le Club de Plongee Suwan Macha, Jean-Pascal Quod	10
LTER_1_Fringing	20151109	Fringing Reef	Moorea	French Polynesia	Ryan McMinds, Becky Vega Thurber	the Burkepile Lab	>35

Thus, after loading and processing the sample and photo metadata files as in the last post, I needed to load these two extra files and merge them with our sample table. This is almost trivial, using commands that are essentially in English:

sites <- read.table('sites_metadata_file.txt',header=T,sep='\t',quote="\"")
data <- merge(samples,sites)
species_data <- read.table('species_metadata_file.txt',header=T,sep='\t',quote="\"")
data <- merge(data,species_data)

And we now have a fully expanded table.

A couple of commands are needed to account for empty values that are awaiting completion when we get the time:

data$relevant_collaborators[is.na(data$relevant_collaborators)] <- 'many collaborators'
data$photo_name[is.na(data$photo_name)] <- 'no_image'

These commands subset the table to just rows that had empty values for collaborators and photos, and assign to the subset a consistent and useful value. Empty collaborator cells aren’t accurate – we’ve gotten lots of help everywhere we’ve gone, and just haven’t pulled all the information from all the teams together yet! As for samples without images, I created a default image with the filename ‘no_image.jpg’ and uploaded it to the server as a stand-in.

Default image shown when a sample has no pictures.

Now I need to introduce the R package that I used to build my map: Leaflet for R. Leaflet is actually an extensive Javascript package, but the R wrapper makes it convenient to integrate my data. The package allows considerable control of the map within R, but the final product can be saved as an HTML file that sources the online Javascript libraries. Once it’s created, I just upload it to our webpage and direct you there!

Note that although I usually use R from the Terminal, it’s very convenient to use the application RStudio with this package, because you can see the product progress as it’s built, and then easily export it at the end.

To make my map more interesting, I took advantage of the fact that each marker on the Leaflet map can have a popup with its own arbitrary HTML-coded content. Thus, for each sample I integrated all my selected metadata into an organized graphical format. The potential uses for this are exciting to me; it means I could put more markers on the map, with tables, charts, interactive media, or lots of other things that can be specified with HTML. For now, though, I decided I wanted the popups to look like this, with just some organized text, links, and a photo:

Acanthastrea echinata: E13.20.Aca.echi.1.20151110

Site: LTER_1_Backreef

Date: 20151110

Country: French Polynesia

Collected by Ryan McMinds, Becky Vega Thurber with the help of the Burkepile Lab.

So, I wrote the HTML and then used R’s paste0() function to plug in the sample-specific data in between HTML strings.

data$html <- paste0('300px; overflow:auto;">',
'<div width="100%" style="clear:both;">',
'<p>',
'<a href="https://www.flickr.com/search/?text=GCMP%20AND%20',data$genus_species,'"target="_blank">',data$genus_species,'</a>: ',
'<a href="https://www.flickr.com/search/?text=',gsub('.','',data$sample_name,fixed=T),'"target="_blank">',data$sample_name,'</a>',
'</p>',
'</div>',
'<div width="100%" style="float:left;clear:both;">',
'<img src="http://files.cgrb.oregonstate.edu/Thurber_Lab/GCMP/photos/sample_photos/processed/small/',data$photo_title,'.jpg" width="50%" style="float:left;">',
'<div width="50%" style="float:left; margin-left:10px; max-width:140px;">',
'Site: <a href="https://www.flickr.com/search/?text=GCMP%20AND%20',data$reef_name,'" target="_blank">',data$reef_name,'</a>',
'<p>Date: <a href="https://www.flickr.com/search/?text=GCMP%20AND%20',data$date,'"target="_blank">',data$date,'</a></p>',
'<p>Country: <a href="https://www.flickr.com/search/?text=GCMP%20AND%20',data$country,'"target="_blank">',data$country,'</a></p>',
'</div>',
'</div>',
'<div width="100%" style="float:left;">',
'<p>',
'Collected by <a href="https://www.flickr.com/search/?text=GCMP%20AND%20(',gsub(', ','%20OR%20',data$collected_by,fixed=T),')"target="_blank">',data$collected_by,'</a>',
' with the help of ',data$relevant_collaborators,'.',
'</p>',
'</div>',
'<div style="clear:both;"></div>',
'</div>')

Yeesh! I hate HTML. It definitely makes it uglier having to build the code within an R function, but hey, it works. If you want, we can go over that rat’s nest in more detail another time, but for now, the basics: I’ve created another column in our sample metadata table (data$html) that contains a unique string of HTML code on each row. In blue, I create a container for the first line of the popup, which contains the species name and sample name, stitched together into a link to their photos on Flickr. In orange, I paste together a source call to the sample’s photo on our server. In green, I create a container with metadata information (and links to all photos associated with that metadata on Flickr), which sits next to the image. And in purple, I stitch together some text and links to acknowledge the people who worked to collect that particular sample. Looking at that code right now, I’m marveling at how much nicer it looks now that I’ve cleaned it up for presentation…

And now that I’ve gotten all the metadata together and prepared the popups, the only thing left to do is create the map itself. However, I’ll leave that for just one more post in the series.

*math not thoroughly verified.

**edit: My father points out that we are essentially building a relational database of our metadata. In fact, I did initially intend to do that explicitly by loading these separate tables into a MySQL database. For now, however, our data isn’t all that complex or extensive, and separate tables that can be merged with simple R or Python code are working just fine. I’m sure someday we will return to a discussion of databases, but that day is not today.

Mapmaking: Part 2

Posted on December 11, 2015 by Ryan

No, you didn’t miss Mapmaking: Part 1. Before getting interrupted by last-minute extra fieldwork with the Waitt Foundation (which was awesome!), I gave an intro to photo management in Lightroom. Today I’ll expand on that, beginning a series of posts explaining how I created this map. On the way, I’ll introduce a little bit of…

*shudder*

coding.

Some really ugly code that I once wrote.

If you’ve been following my blog just to look at pretty beach pictures, I apologize. But I encourage you to keep reading. If any of the code makes you go cross-eyed, don’t worry; it does the same to me. I would love to field some questions in the comment section to make things clearer.

So. I have all of my photos keyworded to oblivion, and those keywords include sample IDs. How did I get them into my map? First, I needed to make sure I could link a given sample with its photos programmatically. I have a machine-readable metadata table that stores all our sample information, which we’ll be using later for data analysis. Metadata just refers to ‘extra’ information about the samples, and by machine-readable, I mean it’s stored in a format that is easy to parse with code. I used this table to build the map because it specifies GPS coordinates and provides things like the site name to fill in the pop-ups. But I didn’t have any photo filenames in this table, because it’s easier to organize the photos by tagging them with their sample IDs, like I explained last post. I simply needed to extract sample IDs from the photos’ keywords and add the their filenames to my sample metadata table. And not by hand.

Excerpt from sample metadata table

sample_name	reef_name	date	time	genus_species	latitude	longitude
E1.3.Por.loba.1.20140724	Lagoon entrance	20140724	11:23	Porites lobata	-14.689414	145.468137
E1.19.Sym.sp.1.20140724	Lagoon entrance	20140724	11:26	Symphyllia sp	-14.689414	145.468137
E1.6.Acr.sp.1.20140726	Trawler	20140726	10:35	Acropora sp	-14.683931	145.466483
E1.15.Dip.heli.1.20140726	Trawler	20140726	10:38	Diploastrea heliopora	-14.683931	145.466483
E1.3.Por.loba.1.20140726	Trawler	20140726	10:41	Porites lobata	-14.683931	145.466483

A popup from the map on our webpage, displaying the sample ID, selected metadata information, and a photo.

To get started, I installed a Lightroom plugin called LR/Transporter. This plugin contains many functions for programmatically messing with photo metadata. Using it, I created a ‘title’ for all of my photos with a sequence of numbers in the order that they were taken. The first sample photo from the project was one that Katia took while I was working in Australia, and it’s now called ‘GCMP_sample_photo_1’. Katia and I also took 17 other photos that contained this same sample, incrementing up to ‘GCMP_sample_photo_18’. The last photo I have from the project is one from my last trip, to Mo’orea, and it now has the title ‘GCMP_sample_photo_3893’.

Then, I exported small versions of all my photos to a publicly accessible internet server that our lab uses for data. I did this with another Lightroom plugin called FTP Publisher, from the same company that made LR/Transporter. Each photo was uploaded to a specific folder and given a filename based on its new arbitrary title. Thus my first photo, GCMP_sample_photo_1, is now easily located at:

http://files.cgrb.oregonstate.edu/Thurber_Lab/GCMP/photos/sample_photos/processed/small/GCMP_sample_photo_1.jpg

Next, I used LR/Transporter to export a machine-readable file where the first item in every line is the new title of the photo, and the second item is a comma-separated list of all the photo’s keywords, which include sample IDs.

Excerpt from Lightroom photo metadata table

GCMP_sample_photo_1	E1.3.Por.loba.1.20140724, Fieldwork, GCMP Sample, ID by Ryan McMinds, Lagoon Entrance, Pacific Ocean
GCMP_sample_photo_2	E1.3.Por.loba.1.20140724, Fieldwork, GCMP Sample, ID by Ryan McMinds, Lagoon Entrance, Pacific Ocean, Ryan McMinds
GCMP_sample_photo_124	20140807, E1.5.Gal.astr.1.20140807, GCMP Sample, ID by Ryan McMinds, Pacific Ocean, Trawler Reef
GCMP_sample_photo_1051	Al Fahal, E4.3.Por.lute.1.20150311, GCMP Sample, ID by Ryan McMinds, KAUST, Red Sea
GCMP_sample_photo_3893	E13.Out.Mil.plat.1.20151111, GCMP Sample, Mo'orea

Now comes the fun part.

To associate each sample with a URL for one of its photos, I needed to search for its ID in the photo keywords and retrieve the corresponding photo titles, then paste one of these titles to the end of the server URL. The only way I know to do this automatically is by coding, or maybe in Excel if I were a wizard. I’ve learned how to code almost 100% through Google searches and trial-and-error, so when I write something, it’s a mashing-together of what I’ve learned so far, and it’s made for results, not beauty. The first programming language I learned that was good for parsing tables was AWK, because I do a lot of work in the shell on the Mac terminal. I thus tackled my problem with that language first, in an excellent example of an inefficient method to get results:

while read -r line; do
search=$(awk '{print $1}' <<< $line)
awk -v search=$search 'BEGIN {list=""}
$0 ~ search && list != "" {list = list","$1}
$0 ~ search && list == "" {list = $1}
END {print search"\t"list}' photo-metadata-file.txt
done < sample-metadata-file.txt > output-file.txt

Ew.

I’ve been issuing my AWK commands from within the shell, which is a completely separate programming language. For the life of me, I couldn’t remember how to use AWK to read two separate files simultaneously while I was writing this code. I know I’ve done it before, but I couldn’t find any old scripts with examples, and rather than re-learn the efficient, correct way, I mashed together commands from two different languages. I then decided I needed to go back and do it the right way, so I rewrote the code entirely in AWK. That code snippet isn’t very long, but it took a lot of re-learning for me to figure it out. So it was about a week or so before I realized that since my map-making had to occur in yet another language (called R), it was ridiculous for me to be messing with AWK in the first place…

So I came to my senses and started over.

In R, I simply import the two tables, like so:

samples <- read.table('sample-metadata-file.txt',header=T,sep='\t',fill=T,quote="\"")
photo_data <- read.table('photo-metadata-file.txt',header=F,sep='\t',quote="\"")

Then use a similar process as in AWK to create a new column of photo titles in the sample metadata table (this time I simply add the first photo instead of the whole list):

samples$photo_name <- as.character(sapply(samples$sample_name, function(x) { photo_data[grep(x,photo_data[,2])[1],1] }))

And now, I have a single table that tells me the coordinates, metadata, and photo titles of each sample. With this, I can make the map, with one point drawn for each line in the table. I’ll continue explaining this process in another post.