Christmas Island Week 2+3 Updates! 🇨🇽🦀

What day is it today? Is it a weekend? Weekday?

I dunno! All I know is that I’ve very much settled into the “island time” that reigns here. My life now moves at a slow, syrupy pace as one day slides easily into the next.

I have been on Christmas Island for three weeks, and somewhere in that time-syrup, I’ve lost track of the Week 2 update (whoops!), so I’ll just roll updates from the past two weeks into one big update here!

Let’s get started!!

Acclimation Aggravations

We left off with me preparing to acclimate my Discoplax celeste (Christmas Island Blue) crabs to my laboratory conditions. During the acclimation week, my crabs were supposed to be kept individually in 10qt buckets along with enough water to prevent any sort of dehydration stress, and my job was to change their water every day. Seems a simple enough task, right?

This wasn’t even its final form! I definitely added more rocks and mesh and rubber bands in order to keep the crabs from escaping.

Wrong! Not long after getting the crabs into the lab, drama unfolded!

Apparently, the larger crabs could escape! Somehow, from being seated at the bottom of the buckets, they could still latch what is essentially their toes onto the lip of the bucket and pull the rest of their body out. I tried everything to keep them contained: fiberglass mesh, rubber bands, heavy metal grids, duct tape, zipties, stones (this potential solution was the most interesting to see them overcome — the crabs were strong enough to not only tear apart the mesh and pull themselves out of the buckets from beneath a heavy metal grid, they were able to still do all this from beneath a stone several times their body weight). I was honestly amazed by how crafty these crabs were, but I was mostly annoyed. #fieldworkfail

Wanted Poster Creator: https://www.tuxpi.com/photo-effects/wanted-poster

This is DC01 after his fifth escape. He’s covered in cobwebs and dustbunnies from hiding out in the storeroom. #foreverontherun His name is Houdini now.

Their escapades were a big problem for my project because I couldn’t really begin acclimating the crabs to prepare them for the experiment if they flew the coop every night — what’s most important for the acclimation period is making sure all the crabs are kept in the same environment for the full length of time. So every time a crab escaped, I had to restart the clock.

Eventually, by combining all the methods and double-mesh-wrapping the especially problematic crabs (here’s looking at you, DC01 and DC11…), I was able to keep them all contained. And with that problem out of the way, I was able to begin my experiment in earnest!

Crab Catching!

While my blue crabs were acclimating, I went out in search of some of the other species I wanted to collect for my project. Specifically, I wanted to catch nipper crabs: the little nipper (Geograpsus grayi) and the yellow nipper (Geograpsus crinipes).

I heard from the Park Rangers that the little nippers were sort of difficult to find — they were essentially all over the island, but no one place in particular, and I had to be a bit lucky to find one. I had seen only one unexpectedly while catching my blues, and the little crab skittered deep into a tree trunk before I even got my crab-catching gloves on.

One morning when I was driving down to The Settlement to get roti canai and curry (did I mention I love roti canai and curry? ‘Cause I do, I really really do!), I saw a dark little crab body dart into the road. Since I was driving sort of fast, I only had a fraction of a second to 1) realize that it was a crab and not some leaf litter blowing into the road, 2) swerve out of the way to avoid crushing the little creature beneath the wheels of my RAV4, and 3) identify the crab in question.

I pulled to a quick stop, turned my car around, and drove back to where I thought I saw the crab as I was driving. Luckily, the little guy didn’t run too far away, and I was able to easily scoop him up in my bucket. Fieldwork victory~

It was a stroke of luck that I found this little crab.

I found the yellow nipper also by accident. I had gone to Ethel Beach and Lily Beach in search of ghost crabs, but had come up empty. Since I wasn’t in the give-up-and-throw-in-the-towel mood that day, I decided to scan the rocky walls at Lily Beach in greater depth to try to search for the crabs. Since the tide was coming in, I had to be a bit careful — the water would be at my ankles one minute and the next, a wave would bring it up to my waist or higher — so I actually began scaling the wall to both look for the crab and also to avoid taking an early morning dip in the sea.

That’s when I saw it! A palm-sized, egg-yolk yellow crab was tucked into a nook in the rock wall. He was perfect, exactly what I was looking for in a crab, but I knew he wasn’t going to be easy to extract. For one, these crabs are called “nippers” for a reason: they may be little, but their pinches are mighty! The nook he was in was also too narrow for me to try to grab him with my gloves on, so I knew I might be risking getting my fingers pinched if I went after him. On top of that, I was about four feet off the ground, clinging to the craggy rock face as the tide was coming in swiftly below me — If I wanted to avoid falling, I knew I would have to try to get to him with one hand.

Challenge accepted!

After about a 15 minute tussle with the little slugger where I used small pebbles to push him to a more open area of the nook, I was finally able to get him to run out. On his way past, he gave me a god-awful pinch and left his pinching claw attached to my finger as he dropped down into the surf below.

After throwing out a few expletives in pain, I climbed down from my perch, grabbed my handy bucket, and scooped him up. We both walked away from the encounter a little battered…he might’ve lost a claw, but the little slugger certainly gave as good as he got!

After a fierce battle, I finally got him! Those little claws definitely pack a punch!

ASIDE: These two beaches are absolutely stunning! I don’t think they’d be fun to swim in since the waves are very wild and the rocks near the shore are sharp and scary, but they’re lovely for walking along.  I took some videos but I can’t seem to upload them to the blog directly — I’ll look into hosting them on Youtube first!

Happy RNAseq Sampling Day 1!

Every day that I have to take tissue samples, I greet my partner with this phrase. Sometimes, he even says it first, adjusting the number to correspond with whatever time point I’m sampling that day. Cute!

At any rate, I was excited and very nervous about sampling the first set of crabs. Would I be able to work quickly enough to avoid degrading the RNA? How long would it take to sample all the tissues? Would it be too late in the day by the time I started on the last crab of the batch? I tried my best to push those concerns to the side as I started on my first dissection at noon.

I ran into a few interesting issues: 1) the tissues all seemed to respond unexpectedly to the RNA stabilization solution I put them into, and I had to figure out how to grind them up without splashing the solution everywhere; 2) the crabs have a single gill that’s oriented in a way that I’ve never seen in any other crab before, so I had to figure out how to count that odd gill along with the regular ones; and 3) each dissection took about 45 minutes, so processing four crabs from start to finish, with very short breaks, ended up taking about 4 hours, which I didn’t anticipate or plan for (I couldn’t stop for lunch! Oh, the agony!!).

The first sampling day was definitely a learning experience, and I’ve since updated my sampling protocol to improve my efficiency and safety, but I suppose that’s what science and field research is all about: being adaptable and learning and improving yourself along the way. My RNAseq sampling days since the first one have all gone smoothly since then, which feels really fantastic. Woohoo!!

Look, Ma! I’m science-ing!

Adventuring to New Field Sites

Since I have a staggered sampling schedule, occasionally I get the day “off”. And, no, that doesn’t mean I get to sit home all day in my jammies binging on “Japanese Style Originator” or Anthony Bourdain’s “Parts Unknown” on Netflix, as I tended to do on my days off back in my regular life. Instead, in the field, my “days off” are actually adventuring days! Since I’m forever looking for a few elusive crab species, on my days off, I pick a new site I want to explore, let a ranger know where I’m headed, and go out into the field for the day!

Having the Garmin satellite communicator has made me feel so safe while on the island. From the middle of a forest, I can text my partner, tease my siblings, and update the Rangers on my status — what a time to be alive!

In Search of Water: Ross Hill Gardens

On my first day off, I wanted to try to find a closer site to collect freshwater from. The site I was going to before was just a little bit too far away, and my water collection trips would take an hour and a half each morning, which is much too long! So to solve this, I went up to my massive Christmas Island map, which I have mounted on my wall, and looked all over for a “spring” icon somewhere near a road. To my great fortune, I was able to find one on the map that was much closer (Ross Hill Gardens; about a 5 minute drive away), so on my day off I set out to find it!

Luckily for me, since small parts of the stream were flowing out of the forest and pooling on the dirt road, I was able to find the site very easily. And when I went into the forest to find a place with high enough flow to fill my containers, I found an ideal collection site about 180 paces in. Perfection!

Discoveries and Disasters at Dolly Beach

On my next day off, a trip to Dolly Beach was on the menu! Dolly Beach is a real trek to get to: you have to use 4WD to drive down (and back up!) two very steep and treacherous hills, and then after that, you still need to walk through the forest for about 50 minutes to get to the beach itself. And although there’s a boardwalk for most of the walk to the beach, it isn’t well maintained at all and has lots of sections that are true trip hazards. Since my first day here when I expressed my interest in going to Dolly Beach to look for crabs (one of my rare species was last collected here!), the rangers have been warning me about the trip — the road down is very steep, and when it rains, it’s impossible for a car like a RAV4 to get back up, and also, the RAV4 engine might not be powerful enough to survive the trek, even on a dry day.

For these and other reasons, I’ve been very hesitant about going, and I definitely didn’t want to go on my own just in case something went south with the car. But one of my new friends here was volunteering for the annual Bird and Nature Week, which brings folks from all over Australia and the East Pacific to Christmas Island to partake in all its natural splendors, and she invited me on one of their tours to Dolly Beach! I excitedly agreed, and also agreed to serve as a “crab tour guide” for the group, so on the morning of, I met everyone on the trail to Dolly and we started walking over.

It was so fun to share my knowledge of crabs with everyone and to talk with the other tour guides about different projects that have happened on the island related to assessing crab biodiversity and population sizes. I also got to see my first female coconut crab as we walked to the beach! Every robber crab I’ve seen so far has been male.

Once we got to the beach, I looked around and definitely felt that it was worth the hike. It was lovely. Very Robinson Crusoe. And it put me in the mind of the island on the TV series, Lost — it was very isolated and it felt that way. But the waters were a sparkling aquamarine, the receding tide revealed small tidepools filled with tiny fishes, and freshwater from somewhere unseen streamed out of the forest and into the sea. So lovely. And there were also tracks on the sand from where mama sea turtles had laid their eggs!

Wilson…? WILSON!!! Dolly Beach definitely gave me that Tom Hanks in Castaway feeling.

This was pretty well-preserved, but we found another with half of the front of the shell still intact!

Dolly Beach at low tide

I could spend all day intertidaling here! I wonder what curiosities I would encounter!

After having a quick lunch and bopping around in the tidepools where I found a cuttlebone and a nearly completely intact nautilus shell, it was nearly time for us to head back. Just as we were turning around, someone yelled something about crabs running into the ocean, and when we looked around, we saw that they actually weren’t crabs at all. They were baby sea turtles!!!

SO FLUFFIN’ CUTE!!! My voice went up like seven octaves the whole time the turtles were on the beach. I couldn’t handle all the cuteness~

Turtle fingers!

We ran like children to watch the cute little turtles run towards the sea, their flippers awkward and adorable on the golden sand. Some were going the wrong way, so we lifted them up and placed them into the shallows — it was amazing how much better they were at swimming than running! We also went back to their nest and rescued a few stragglers that had gotten caught in the fallen debris and scared away a nearby coconut crab that looked to be eyeing the turtles for lunch. And then once all the turtles were safe at sea, we walked the 50 minutes back to the cars.

Since I had space in my car for a few others, a Singaporean couple and I began the difficult drive up the steep hills. My car seemed to handle it well, but once we reached the top, there was smoke coming out from under the hood. Uh-oh…

Once all the cars had ascended, we kept driving out of the forest towards the main road and the car seemed to be fine. But then, all of a sudden, it didn’t, and it seemed to be working very hard to maintain a normal speed. In quick succession, the check engine light came on, the car smelled like it was burning, and the entire jalopy ground to a halt and couldn’t be restarted. #ded

Fortunately, me and the Singaporean couple were able to hop into one of the other cars from the tour, and we left Goldie sitting on the side of the road. Later that day, I had to call the car rental company to retrieve the dead car, and they also gave me access to another vehicle, so all’s well that ends well, I suppose!

Back at the Pink House Research Station, the tour group got to wander around and talk to me and the other researchers about our projects — it was so great to see how excited people were about my research! Yay #scicomm! It made me really exited for the “Meet the Researcher” night that we’re having tomorrow for everyone in the Christmas Island community!

Taking it Easy

All work and no play makes Vicky a dull girl

or so I’m told.

These past two weeks I’ve finally had the opportunity to just enjoy the island. I’ve gotten to eat more local foods (Lucky Ho’s is my new favorite restaurant, and it isn’t just because it’s colorful, although that was a huge influence on my deciding to visit in the first place), go to my first outdoor movie on the island (I watched Baby Driver; bad movie, but the outdoor cinema didn’t feel outdoors at all!), and go snorkeling with my new friend in Flying Fish Cove.

Beautiful banister outside of Lucky Ho’s. Their Chinese food is so delicious!

Outdoor Cinema before the show started. The audio quality was surprisingly great!

I think I really fell in love with the uniqueness and the beauty of the island when I went snorkeling that day. It was late afternoon, sometime near the golden hour, and my friend and I were swimming in these glorious turquoise waters over a stunning coral reef. At some point, I heard a sound like a song from the surface, so I lifted my head out of the water and listened to the eerily beautiful afternoon call-to-prayer emanating from the town mosque. In that moment, I looked around me at the shifting afternoon skies, the blue-green infinity beneath me, and the verdant rainforest climbing recklessly up the side of the golden limestone cliffs of the island and I felt something move inside of me. While feasting on that sensual smorgasbord, I felt the magic of this island, and I felt gratitude welling up inside of me that I had been given the opportunity to experience a place so special.

I can’t believe this is really my job!

Flying Fish Cove, Christmas Island. This color palette makes my eyes very happy!

The water was so clear and so turquoise. It was absolutely stunning!

-Vicky

Japan 2018: A Walk in the Woods [Nakasendo Trail]

“What the hell am I doing?”, I asked myself, frantic. It was 4am, I hadn’t yet slept, and I was rushing to gather the last of my gear in a daze before my Lyft arrived. “What the hell am I doing? Is this really happening?”

Amazingly, the fact that I was really, yes, really, going to Japan in a few hours didn’t register until that exact moment, hence the panicking.

I’ve wanted to go to Japan in earnest since early high school. I have distinct memories of downloading the first editions of the Genki textbooks my second year and trying to pick up whatever bits of the language I could. I took Japanese on and off throughout college, and when I enrolled for grad school, I picked it back up with gusto. I now take around 3 hours of Japanese every week and I love it.

After I passed my PhD qualification exam, I decided to finally pull the trigger and buy my tickets to Japan, bringing this dream of mine sharply into focus. I’m writing this now on the Hikari super-duper high-speed train (+200mph) as it’s literally screaming its way across the Japanese countryside en route to Kyoto. Not long ago, I finished hiking the lovely, historic Nakasendo Trail (more on that below). I’ve been in Japan now for about 30 hours and I already feel like I could stay here exploring for years.

Yesterday was…an extra long day. My flight from Sacramento left bright and early at 6:55am, then after a brief layover, the flight from LA to the Haneda Airport in Tokyo took another 11 hours.

(Below: Japanese toilets are the best toilets! They’re warmed, they play a soundtrack of a rushing river as you tinkle, they squirt warm water to clean you off, and then they blow air on your bum until it’s all dry! This was one in the airport in Haneda. We’re seriously missing the boat on this, America!).

After arriving at around 3pm local time, I wandered around the airport looking for the post office to pick up a data-only SIM card I arranged to have delivered before I left the states, then I activated my first rail pass (bestowing me with free unlimited rides on nearly all Japan Railways routes), then changed money in Shinjuku, then took the Shinkansen Hikari to Nagoya, then a local train to Nakatsugawa (that I missed twice because I was honestly a sleepwalking zombie by that point), and finally a taxi to my hotel. I got to my room by 11:25pm.

All I wanted to do was undress and pass out in my bed at least until the next century, but my hotel had a public bath that stayed open until 2am that I wanted to experience too, so I washed up in my room, changed into the yukata that the staff left by my bed, and clomped downstairs in my slightly too small borrowed slippers to the bathhouse. A sweet Japanese girl gave me a crash course in bathing in public in Japan and after a split-second of self-conscious hesitation (because honestly this ain’t my first [publicly nude] rodeo), I stripped down to my birthday suit and hopped in the bath.

After the grueling day (days??) of travel I had, the hot water felt absolutely divine. Tension melted away from my sore muscles and feet, and it felt like my entire body let out a relaxed sigh as I soaked. When my fingers started to get pruny, I got up, dried off, and went back to my room. I passed out as soon as my head hit the pillow.

(Below: Views from my hotel room in Nakatsugawa, Gifu Prefecture)

In the morning, I met my new friend for breakfast and we had a surprisingly effective conversation — she spoke to me in English and I responded to her in Japanese. We knew just enough of each others’ mother tongues for us to discuss things like hometowns, places we want to see in the world, jobs, pets, and family. I felt so happy when I was able to use my broken Japanese to describe my research to her — she seemed genuinely interested in my work on the land crabs!

After we parted, I checked out, hopped on a local bus to the station with other foreigners planning to do the Nakasendo for the day, and headed to my first location — Magome.

The Magome-Tsumago Trail (called the “Nakasendo” — the central mountain road) is part of a historic path that pilgrims used to walk from Kyoto all the way to Tokyo in the Edo period, a journey that usually took about ten days and passed through 69 towns. This part of the trail is a site of special historic significance and the buildings along the way have been preserved to look exactly as they did long ago. Thankfully, instead of ten days, this small section only took 3.5 hours and passed through around 8km (5 miles) of lovely forests near rushing streams, rice paddies, and micro-towns with quaint tea shops that greet foreign visitors with piping hot cups of tea. It was absolutely lovely and so peaceful. Here are some of my favorite photos from the hike:

It’s so gratifying to be able to carry out simple conversations with people in Japanese! One conversation that stood out for me from the hike was one I had with a 74-year old man who owns a dumpling shop in Tsumago. He told me (all in Japanese) that he and his family had lived in the area for many years and that he doesn’t often see women walking the trail alone (he said he’d only seen about 4, including me, this whole week!). He said he thought he was too old to learn English now, but that my Japanese was very good (spoiler alert: it kinda isn’t, but the Japanese are very kind). I told him about my family and hometown, where I go to school, my plans while I’m in Japan, and what I thought of the trail. It was so fun! I can understand a lot more than I can say (I found myself laughing out loud after overhearing a group of school girls tell jokes to each other on the trail), but I’m challenging myself to speak Japanese as often as possible so I can get better!

Over the next four days, I’m all set to wander around Kyoto. In addition to lots of temple and shrine visits (Fushimi Inari Taisha, here’s looking at you, beautiful! 😘), I’m planning to watch a springtime geisha dance, visit local shopping arcades, and the Arashiyama Bamboo Grove.

行きましょう!😊

(Week 1 Update) The Final Fortress in the Kingdom of the Land Crabs

A Taiwanese crab biologist once called Christmas Island “the final fortress in the Kingdom of the Land Crabs”. After being on the island for about a week now, I think I’m beginning to understand his sentiment. Land crabs the world over are threatened on all sides by habitat destruction, invasive species, and overexploitation, and their populations are in a steady decline in places where they once lived abundantly — in that light, Christmas Island, which is literally crawling with land crabs, does feel like a final stronghold of sorts. Or maybe it’s the way the imposing tiers of limestone cliffs that compose the island make me feel like I’m entering a terraformed castle that was thrust up from the ocean floor millions of years ago whenever I venture into the forest. But more than that, I think I understand his meaning most strongly when I’m standing, awestruck and silent, in the thick of one of the rainforests on the island, outnumbered one million to one by Christmas Island red crabs and coconut crabs — this place is not mine. I am merely a visitor and this place, this incredibly wild, incredibly beautiful, sometimes dangerous place, was not made for me. It’s theirs. It is their stronghold, it is their birthplace, it is their home. Christmas Island belongs to its crabs.

If you’ve been following my story for a while, you’ll know that I study land crabs for my doctoral research, and you’ll probably have already guessed that my coming to Christmas Island is the realization of so many of my dreams. I feel like a kid in a candy store here — every trail I’ve gone down on the island has brought fresh discoveries and borne new scientific questions, and my passion for understanding the evolutionary histories of these crabs has been fanned to new heights since I’ve arrived.

In short, I’m having a blast!

Here’s my Week One Update (August 12th – August 22nd)!

The Trip

…was SO long! I left my house in Davis at 5PM PST on August 12 and didn’t actually arrive on Christmas Island until 2AM PST on August 15th, meaning I spent two and a half days in transit. I drove from Davis to San Francisco, flew from San Francisco to Sydney, got stuck at customs in Sydney (apparently my empty 20L liquid nitrogen freezer raised a few of the wrong sorts of eyebrows), then flew from Sydney to Perth, and then from Perth to Christmas Island. And yes, it did feel as awful as it sounds. Traveling all that long way with little restful sleep on a diet of crappy airline “food” and with seven very heavy pieces of baggage in tow was no treat, but I was fortunate enough to meet a few people that made the trip bearable and even a little enjoyable.

While in Perth, I met up with some researchers from the University of Western Australia that were able to fill my freezer with liquid nitrogen (which I need for my research on the island), and I also got a fantastic tour of the collections at the Western Australian Museum from the curator of the Crustacea there. It was a joy to talk about my Christmas Island research plans with the curator and some of the other museum staff, and honestly, the cup of caffeine he gave me before I had to head to the airport again was a godsend. Australians are such friendly people! What amazed me most at this point in my journey was how global and connected research is these days — from the US using only email, I was able to coordinate all of this indispensable research support and arrange to have all of the liquid nitrogen (which, at that quantity, is classified as a dangerous good) sent over to Christmas Island. It really blew my mind to see it all work out so flawlessly.

Rose quartz and serenity skies on the way to Sydney. The view of higher clouds makes all the stress of traveling worth it.

First Night on Christmas Island

I felt like I was floating when I saw this. Extreme sleep deprivation? Possibly. But more likely it was my utter excitement at having made it this far in my journey — it was really happening!!

After I landed, I met the Chief Ranger of the Christmas Island National Park outside of the airport. He greeted me warmly, helped me load all of my heavy things into my rental car, gave me a crash course on driving an Australian vehicle (everything is reversed!), and then I followed his car to the Parks HQ. Since I’m staying at the Pink House Research Station while I’m on the island, which is operated by Parks Australia, once we reached HQ, the Chief Ranger gave me my keys, a map of the island, instructions on how to reach the Pink House, and two large cans of bug spray for the “mozzies” (a.k.a. mosquitoes, of which there are legion). I then hopped back into my car and drove over.

Road to the Pink House Research Station. This place is literally all jungle.

As soon as I turned off the main road and started driving through the jungle track, I finally began seeing my first land crabs! I drove by 11 coconut crabs on that first drive alone! Once I reached the Pink House and unloaded all my gear, I took a tour of the grounds and was utterly amazed by how many coconut crabs there were. Afterwards, I went back inside, unpacked a few things, called my family and my boyfriend to let them know I made it over safely, made a quick (but super yummy) dinner, and crashed. Hard.

First meal on the island! I’m sad I only brought one #10 can of Chicken a la King — this meal was super~

Getting Started on Research

Once I woke up from my weird, jet-laggy slumber, I was ready to get started on my projects! But first, I had to coordinate with the Park Rangers about collecting my animals. The rangers have a system that they use to check on the teams that are heading into the field to make sure no one gets lost or forgotten about, so they briefed me on their protocol and on some other important safety issues on my first full day here. After the safety briefing, I went on a fantastic tour of the island and found out more about its history, the townsfolk, and some of the work that the Rangers do to maintain the park (they do so much!! The park is nearly 70% of the whole island!).

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The Settlement, Christmas Island. Beautiful view from up near the Park HQ.

The next day, I tried to locate my crabs. I’m working with seven different species of land crabs, so there were (and still are) a lot of sites I need to check to find them all.  There were a few leads the Rangers told me about that I followed up with first, and then there were other collection sites I had read about in the crabs’ species descriptions that I wanted to check out too. I couldn’t help but feel like I was playing the real-life version of The Safari Zone from those old Pokemon GameBoy games, looking for rare specimens all around the park! And I really loved gearing up for the field that first day! Here’s a picture of me and all my equipment right before I left for my first site survey.

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So ready!

The first place I checked out was called The Dales, which is a series of freshwater streams at the western edge of the island. I heard that one of my primary research animals (Discoplax celeste, the Christmas Island Blue Crab) was found here, so I was stoked to see this species in real life.

Once I got to the Dales, I had to use 4WD to get down to the trailhead, which was both really fun and a little scary! And then as I entered to forest, I saw red crabs crawling from everywhere! They were running in and out of holes in the worn limestone boulders, and I couldn’t help but wonder what secret missions each frantic little crab was on.

When I reached a small stream, I finally saw the blue crabs! There were so many of them peeking out from their burrows in the riverside. My first trip into the field ended up being a resounding success!

My field site at The Dales

Over the following days, I went back to The Dales several times to collect the crabs I wanted to use for my experiment. Once I collected them all and got them set up in the lab, my RNA sequencing experiment officially began! Woohoo!

My face after catching the last of my blue crabs. Muddy, hot, and happy!

Cute little blue crab hiding in her burrow!

My field lab! The crabs are acclimating on the left, and my molecular lab is set up on the right.

Currently…

Here’s my daily schedule now that my primary experiment is finally up and running. Since the crabs are acclimating now, I only really need to do water changes every day, which gives me quite a bit of time to work on some of the other projects I’m doing on the island, but next week when they’re actually going to be in their experimental treatments, things will get a lot busier for me!

6:30AM: Wake up, FaceTime loved ones, check email, update social media (I think I’m really getting the hang of Twitter!)

7AM: Eat breakfast!

Mountain House’s Biscuits and Gravy meal is so. so. yummy. And so filling!

Most of the time, I eat one of the meals I brought from the US but sometimes I treat myself to roti canai by the seaside. I really love roti mornings!!

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I ❤ roti canai. Been craving this taste since I left Singapore last summer!

Flying Fish Cove, Christmas Island

8AM: Check for escaped crabs in the lab. Do a happy dance when all the crabs are still in their buckets, or alternatively, creatively string together profanities while crawling on hands and knees in the dusty, cobwebby storeroom looking for escapees. I’ve been happy-dancing a lot lately, so I think that’s a great sign!

9AM: Drive to get freshwater for the crabs. There are 23 crabs now, and each needs 1.5L of water every day, so I have to carry about 35L (~10 gallons) of water from the stream to my car (i.e. every day, I work super hard on my fieldwork body 💪🏽). The drive to the spring is absolutely lovely though — this is what I pass every day on the way there:

12PM: Eat a quick lunch and start doing water changes for the crabs. Crabs poop A LOT, probably a lot more than you’d realize!

2PM: Watercolor time~🎨~ I’m absolutely awful at it, but I love playing with the colors. It’s a nice way to relax between science-ing sessions.

So inviting!

3:00PM: Pick a new field site and go on an adventure! Sometimes I go out to collect data on coconut crabs, and at other times I go looking for some of my rarer species. Occasionally, I go out to see a new wonder on the island, or to just observe the crabs doing what they do in nature. I really love adventure time!

Evening: Eat dinner, update social media, check emails, shower, work on things for my PhD — right now, I have to do a lot of reading and writing for an exam I need to pass to become a full PhD candidate — and then I go to sleep! Next week, I’ll actually be doing a large portion of my sampling, so I’m really excited for that. I’ll post another update blog in about a week!

Until then, if you want to keep up with my adventure in real time, follow me on Twitter @origamicrab!

-Victoria

Adventure is out there!

It’s [almost] adventure time! Ten days until Christmas Island

All day long, I’ve been dreaming.

With my Christmas Island expedition going live in less than two weeks, my many, many to-do lists have been getting shorter and shorter. I’ve purchased all of my research supplies and rations, finalized all my experimental protocols, paid for my accommodations and my 4WD rental, gotten approval for my collection and export permits, and have almost completely packed my bags and field crates.

As a Type 1 Diabetic, doing an expedition of this sort also takes lots and lots of forethought and planning with my doctor, so I’m happy to say that all of those details have been finalized too! Three cheers to the Dexcom continuous glucose monitoring system and the Medtronic MiniMed 630G insulin pump for giving diabetics like me the freedom and peace-of-mind to follow our wildest dreams!

In the wake of all my planning, a quiet has recently settled over me, a kind of peace that comes with being as fully prepared for this thing as I think I can get. So lately I’ve been giving myself a little time to daydream.

I’ve imagined myself driving out into the rainforest for the first time to find ideal field sites, or hiking to one of the islands many beautiful natural waterscapes to collect Christmas Island blue crabs. I’ve tried to imagine what those places might smell like…like rich, dark soil, or maybe a little bit like rain.

 

https://www.crabdatabase.info/data/original/brachyura/eubrachyura/thoracotremata/grapsoidea/gecarcinidae/discoplax/discoplax-celeste/live/discoplax-20celeste-202.jpg

Discoplax celeste, the Christmas Island blue crab. They like hanging out near waterfalls and freshwater springs. (Image credit: http://bit.ly/2vlqinF)

I’ve dreamed about how the thick, warm, heavy, humid air will feel against my skin as I move through it, and about how lovely an ephemeral breeze will feel after a long walk through the verdant trees. And in my dreamworld, I can almost hear the hundreds of unseen land crabs scuttling across mossy rocks and damp roots and the complex songs of many strange, colorful exotic birds. But since I know no half-remembered daydream will ever come close to what reality has in store for me, I’ve also been trying to take a more “useful” approach to my imaginings by mentally rehearsing my field experiments and collection procedures for the 8 different research projects I’ll be working on during my month and a half on the island (8 projects — is it ambition or masochism? You decide! 😉). I know things might turn out differently once I’m there, but I’ve found that visualizing my workflows is still a comforting thing for me to do. As I like to say, fail to plan, plan to fail! 💪🏽

Image result for the grotto christmas island

Grotto at the magnificent Dolly Beach, one of Australia’s top ten best beaches (Image credit: http://www.101bestbeaches.com/wp-content/uploads/2016/11/Christmas-Island-12.jpg)

I’ll certainly have a lot to work on while I’m there, but I think the best advice I’ve heard so far about doing fieldwork in a place like this is that I should remember to take time to just BE there, to give myself the space to experience the island and the animals and the thrill of being almost completely disconnected in such a beautiful natural setting. Apart from me being able to observe natural history details about the crabs and their habitats that I might otherwise miss, I think just existing in this place will also teach me about myself… about my resilience, my strength, my limits, my drive, and my dreams. This journey will hopefully be one of scientific discovery AND of self-discovery, and no matter what happens, I’ll come away from it knowing something new!

-Victoria

 

P.S. Within the next few days, I’ll be posting information about how you can follow my journey while I’m in the field using the satellite tracking functionality of my Garmin inReach SE+.

 

I’ll also be posting cool stories, pictures, videos, walking trail routes, and personal reflections live from the field to this blog and its associated Twitter account (@origamicrab) once my adventure begins. Make sure to follow me to stay updated! 😊

 

Featured Image Caption:Gecarcoidea natalis, the Christmas Island Red Crab. I’ll be studying this and six other species of terrestrial crabs while I’m on Christmas Island. (Image credit: https://parksaustralia.gov.au/christmas/images/home-1.jpg).

 

 

 

 

 

[Reflection] ANGUS 2017: Analyzing High-Throughput Sequence Data Workshop

About a week ago, I had the opportunity to participate in an intensive, two-week long workshop offered by the Data Intensive Biology Summer Institute (DIBSI) at UC Davis that taught me how to analyze genomic and transcriptomic data sets, which tend to be very large (in terms of computer storage units, these data sets are often multiple gigabytes or sometimes even entire terabytes in size) and hard to handle. With recent breakthroughs in sequencing technologies that are making it easier and cheaper every year to read your favorite organism's entire genetic code base pair-by-base pair, I think we can truly say that we're living in the golden age of biology. And while this means that we can now begin answering the deepest questions about how life on earth evolved or discovering ways to alter genetic sequences to improve the welfare of our species and those that share the planet with us, the simple truth is that with all this power, we're capable of collecting more data than we sometimes really know what to do with.

Image result for nanopore

Therein lies the power in ANGUS and other workshops like it (check out Data Carpentryfor more info). These workshops take researchers that have big, bold, beautiful dreams about how we can utilize these often overwhelmingly large genomic datasets to understand our world in new, intriguing ways, and gives them everything they need to be successful in their scientific pursuits. But more than that, they teach the participants how to avoid major pitfalls and frustrations that often discourage scientists from exploring the genomes of their research organisms in the first place.

In short, the trainers at these workshops are miracle workers.

But before I tell you in full where the workshop has taken me, I'll tell you first where I began.

Before I started ANGUS, I was terrified of coding and the command line. Trying to do even simple tasks using Terminal or R brought me serious anxiety, and in my graduate coursework, I never felt the Imposter Syndrome as strongly as I did when we had to complete assignments in R…I felt as if all my classmates sailed through the assignments while I puttered slowly along, getting more and more discouraged with each little error in syntax. Honestly and embarrassingly,  I thought it was something only "smart" people did (even as I write that now, I feel foolish). Worse still, in my head, I had this incorrect picture from popular media about who a coder was and what a coder looked like (usually male, usually white, usually an ace at all things mathematical, precise, and rigid), and I never thought I fit that bill in any way. I revel in subtleties, in the qualitative, in description, in prose. And I felt like coding could never be something I could be interested in, let alone be any good at.

But on my last day of ANGUS, when I looked around at all the diverse faces in the lecture hall, at all the women, the men, and the gender non-conforming, at the students from Italy, the UK, Japan, Kenya, Brazil, and all over the US, what struck me most was that, after our experiences at the workshop, we were all coders. We could all do it. I realized then that anyone can do it, and that was ANGUS's biggest gift to me. Well, that…and the pages and pages of notes, all of the know-how, a Rolodex chock-full of high-powered, helpful, friendly bioinformaticians, and a ton of usable, operational, clearly notated scripts and lines of code…but the huge boost in coding confidence was a definite plus!

Now when I sit down to bioinformatically examine data, I feel excited and confident, driven to identify patterns in the data that further pull back the veil of the biologically unknown. Every successful line I run gives me affirmation. And even when I run into errors, instead of shutting down in a cold sweat, the part of my brain that loves to solve problems lights up, and I use the resources I learned at the workshop to debug my code.

How incredible a thing is that? ANGUS took me from zero to bioinformatic hero in two-weeks time. If that's not a miracle, then I don't know what is.

 

Resources

If you're interested in working on improving your own proficiency with analyzing high-throughput data, all of our lessons from this year arefreely and publicly available online! Why not give it a try?

-Victoria

P.S. If you're working through the ANGUS lessons and you run into trouble, shoot me a message with your error codes and we can debug them together! 🙂

P.P.S. Go tigers, go!!! (Note: the adorable featured photo is in reference to the three training rooms used at the workshop: Room Lions, Room Tigers, and Room Bears (oh my!))

P.P.P.S.

 

Lions, tigers, and bears, oh my! (DIBSI Bioinformatics Training Workshop)

bioinform imageFor the next two weeks, I have the privilege of participating in a data intensive bioinformatics training workshop at UC Davis called ANGUS (Analyzing Next-Generation Sequence Data), and I’m so excited to learn some new computing skills! In this workshop, I’ll learn how to analyze huge amounts of sequence data, starting from the basics of using the command line and moving all the way up to using complex programs that can survey an animal’s genome to reveal fascinating evolutionary patterns and processes. From the course website:

Students will gain practical experience in:

  • Python and bash shell scripting
  • Cloud computing/Amazon EC2
  • Basic software installation on UNIX
  • Installing and running Trinity, BWA, Salmon, SPAdes, ABySS, Prokka and other bioinformatics tools.
  • Querying mappings and evaluating assemblies

As of now, I have a very vague idea of what all of that means, but by the end of next week, I’m hoping to be fairly proficient with it all — how fantastic! For my RNAseq study on the land crabs of Christmas Island, these skills are absolutely essential, and seeing as my current skills with coding and bioinformatics are okay at best, I stand to learn so much from this workshop.

Follow my journey with #TeamTiger on Twitter at @origamicrab or via the workshop hashtag, #ngs2017!

Electric Blue

I wrote this piece a few years ago shortly after I finished my first open-ocean dive on a shipwreck in Tulamben, Bali. To this day, this is still one of my most cherished memories, and my experiences that summer were key to me becoming the scientist I am today, so I thought I’d share that memory here with you! Enjoy 🙂


In the beginning, it was awkward. Everything about it was awkward, uncomfortable, foreign. The weights around my waist. The heavy metal cylinder strapped to my back. The dense twists of tubes that attached every which way on the jacket that was more of a balloon than a vest. The fins that made me look like some freak penguin out of a science fiction horror flick. On the shore fully clad in my gear, I felt like a fool, and more than once I thought, “Vicky, what in the Sam Hill do you think you’re doing out here?!” After the 16 hours of pool and bookwork, it was finally time to put everything to the test in a body of water that had no walls and, although also strongly flavored, wasn’t doused in an unhealthy amount of chlorine. It was time to dive.

As my instructor started the five-point descent with me and my new dive buddy, Dawn, I felt my excitement quickly outpace my apprehension, and I deflated my BCD and started to sink. The next forty-five minutes were nothing short of life-changing. The awkwardness was replaced by a logic — down here, the gear just fit. It wasn’t heavy, or burdensome, and the fins, the little devils that they are, proved to be one of the most important parts of the entire get-up. By the end of the day, I loved them, and I swam to shore on my back as I watched the salt water sluice over them as I flutter-kicked. But I digress.

As soon as I dipped my head under the water, I thanked all my lucky stars that I was able to buy goggles with prescription lenses. What I saw was incredible. Dozens of other divers swam in schools around the sunken USS Liberty wreck site that was literally more coral than wood. The bubbles from their regulators spun in dizzy whirlpools to the surface as they wove in and out of the wreckage. I was amazed at all the coral, and even more amazed that I could identify a bunch of them! As I was thinking about which page in “Corals of the World” a particular colony was on, I heard my instructor rap on his cylinder to catch my attention. He pointed up, and a meter above my head, a giant school of jackfish were circling between me and the atmosphere I had left behind. I rotated onto my back and swam underneath them as I marveled at how the surface was sparkling 18 meters above me.

I turned my attention back to the coral — my Seriatopora, my Acropora, my Pocilloporidae, and all my Faviids. They were lovely, so lovely, and living. On the wreck, I saw no bleached corals. But I did see a sponge that I could fit my head inside of. I did see tunicates that dotted the reef-wreck like stars. I did see fish that wore the entire spectrum of visible colors (and invisible ones — some reef fish can fluoresce) like cloaks over their scales. Everywhere I turned over the wreck, there was a new wonder to behold, some new microcosmic universe that beckoned exploration. I saw Gill, Dory, and Nemo everywhere, as well as my little dottybacks that I’m researching in the lab. Those fish in particular were spectacular — they shone a bright, electric blue that could easily put sapphires to shame.  I blew regulator kisses at fish that came within less than a foot of my face in curiosity, and followed carefully behind a pufferfish that was wider around than my midsection. In short, those were the shortest forty-five minutes of my life.

Back at the surface we ate a hurried lunch to prepare for our next dive. I asked my instructor why we ascended so soon (it felt like we were underwater for maybe 20 minutes, tops), but he assured me that we were bordering on 50 minutes by the time we swam from the wreck. Oh, how time flies! I finished my lunch (Nasi goreng – fried rice) and took my blood sugar. Diving with diabetes is a little more involved than diving without it, so I made sure my test results were all in line before suiting up again to visit the Coral Garden.

I couldn’t think of a better name for this dive site if I tried. Coral sprung from the most unlikely nooks and crannies like little aquatic weeds. Imagine 100+ square meters of coral — just coral. No rocks, no trash, no plain surfaces of barren, boring sand — just coral. I felt like I’d died and gone to the only heaven I could have imagined for myself. I floated like a seraph over the reef, pointing here and there at particularly lively bunches of coral. I saw a giant eel curled up inside of one, flexing its jaws. And there were giant clams that flaunted their splendid lips like the divas they are (fun fact: these clams have symbiotic algae that live in their tissues too — just like the coral’s zooxanthellae!), and so many anemones that it looked like they were all just one undulating mass of stinging tentacles. Further down, someone had placed metal substrate in the sand in the shape of an airplane to create an artificial reef for the coral, and boy, did they take to it. It was absolutely spectacular.

Yet again, the forty-five minutes washed by and it was time to leave the water for the day. I waved goodbye to the reef as I reached toward the twinkling surface and flutter-kicked myself upward. Far too soon, I was floating, and I took a deep breath of surface air. Back at the resort, I washed my gear and got ready for the two hour drive back to Sanur from Tulamben. All along the way, I slept (except when we passed the giant volcano and the monkeys that were playing a game of chicken in the middle of the road), and all I could dream of was the paradise that was quickly falling behind me as we drove away.