What killed the harbor seals?

My time as a Ph.D. student in the Vega-Thurber lab has come to an end. Completing my dissertation was a very exciting and relieving moment in my life.  To add to this excitement, just a few days after my latest paper from my dissertation was published in the Journal PeerJ. This paper was an extension of the work that I talked about on a previous blog.


Celebrating the completion of my P.h.D

Celebrating the completion of my P.h.D

In my last paper, I looked at the bacteria and viruses from a group of seven young harbor seals that died from some unknown brain disease. When veterinarians performed a necropsy (the animal version of an autopsy), it appeared that these animals were infected with viruses. Although, when we used high-throughput sequencing (sequencing of large amounts of DNA or RNA) to identify a virus we did not find any. The lack of viruses in my results was very surprising as well as disheartening. See I wanted my research to revolve around characterizing viruses, but given that, I could not find any viruses this inhibited my grand research plans.

This situation is very common in research; our hypotheses are not always correct and we often get negative results. It’s one of the aspects that makes the work of a scientist challenging, but it also keeps us thinking and generating new ideas.

My next step was to refocus my question and approach. If a virus did not kill this group of animals something else did. Now I had a new question to answer. What killed the harbor seals? To answer this, I examined the genes of the seven harbor seals. I used a sequencing technique that is known as transcriptomics or RNA-sequencing. This technique is a high-throughput sequencing approach looking at all the genes in a sample. In my case, I was examining the genes in each of the seven seals that died from the mysterious brain disease.

I then analyzed the genes of the harbor seals using computer programs, statistics, and biological principles (bioinformatics). To my surprise, all these animals had high levels of genes related to fatty acid metabolism. Unexpected results are also a common occurrence in research. I initially believed that these animals died from a virus, but my results were suggesting that they likely died from a metabolic disease!

What does high levels of fatty acids in the brain signify?  Generally, fatty acids are important for building cells and providing energy to cells. Fatty acid gene activity typically takes place in fat and the liver cells, and large production of these gene types may indicate a metabolic disease. Things that trigger high fatty acid production includes poor nutrition intake or exposure to toxins. So, we think that these animals either did not absorb proper nutrients or encountered a toxin that caused high fatty acid metabolism production in their brains, which may have led to their death.

So now that we know that fatty acid metabolism dysfunction can occur in the brains of marine mammals we can begin to monitor these genes in other marine mammals. We can look for the same fatty acid genes that we found in our study in other animals. This will help us better understand this disease and hopefully prevent the deaths of other animals. Interestingly, when I began this research question, I envisioned the final results of my study very differently. I didn’t expect to examine marine mammal genes and metabolic pathways, but research has a mind of its own and leads us to unexpected and exciting findings.

Tempers flare and temples collide

Wonders of being a Wallflower

One of the more interesting things about this whole experience is working with a crew that doesn’t speak your first language regularly. I recognize that for non-English speakers this might be something commonly experienced, but for me this is a first. This has led to dramatic alteration of my personality. As you might have been able to tell from this blog, it’s hard to get me to shut up. But on this voyage I have been uncharacteristically taciturn, shy even. I know it’s hard to imagine. Honestly even after 4 weeks, I haven’t yet come out of my shell and haven’t yet figured out how to behave most social situations. I suspect most people here think I am psychotic. You’re there, 15 people are talking at a rapid pace in French, talking about something, you have zero idea what although you did catch one word, your name, and then everyone laughs. They all then look at you. Um. What do I do? What do I do? Do I laugh too? ‘Oh yeah! Ha, ha, ha. Whatever it was that you said was hysterical!’ Do I maintain the somewhat blank-faced half smile I normally carry around, that probably looks like I once had a lobotomy, on my face? Or do I just keep staring at my pancakes and pretend that I wasn’t paying attention and hope everyone stops looking at me? Depending on how tired I am and who is sitting next to me, I pick at these choices randomly.

Loic and sunset

Now while this has its drawbacks, I have found that this alteration in my personality (aka not being an insufferable know-it-all and blabber mouth) is quite beneficial. First, you get to experience your inner voice in overdrive…hence this blog. I generally find topics to write about while immersed in long self-induced silences when a) its meal time and there are 15 French people speaking about various things simultaneously b) long boat rides while everyone is speaking French and c) on the deck while getting ready to dive when everyone is speaking French. Now I know some of you said that a great way to learn French is direct immersion. I’ve been deeply immersed for the last 4 weeks, and I’d say emphatically this is not true. Whoever said this has never truly been immersed I think. It is really hard to understand a language while its spoken rapidly by many people all about different things and not always with any context. Also this is a language that doesn’t pronounce most of the letters in the word, so even if I might have seen the word in the books I am reading in French, I’d never even know if anyone even said that freaking word. After many weeks immersed I’d say I can get maybe a few words if there some context or if people gesticulate. Otherwise I just get the noise the peanut characters make when talking on the phone “whan wha whan whan wan, Becky, hahahahah.” They’re making fun of me in French again aren’t they?

Current anchorage pano

I’m a spring breaker on the Tara

But other than my internal monologue being tuned to high, being quiet, I found, has been useful for another reason. I am totally not in charge. No responsibilities really. Nada. I am so incompetent language wise, I basically just sit around and wait for people to tell me to do stuff. People who know me…ponder that for a couple minutes.  Me…waiting patiently for other people to tell me to do stuff. And even more shocking…then me doing it without offering an alternative opinion or making a wise crack about the plan. I know…. it’s hard to imagine. I too keep marveling at my ability to keep my trap closed. I have to say this has been awesome. I don’t have to make any choices! I don’t tell anyone what to do. I don’t have to make plans. I don’t have to drive the boat or trailer, badly. I don’t have to cook dinner or remind people that is not the way you cut onions. I don’t need to wake people up (cough, Rory) or make sure they (he) gets on the (his) plane. I don’t have to tell anyone to put on sunscreen (cough, Ryan), to stop cheating at cards (cough Stephanie), or to stop eating all our week’s worth of food in one sitting (cough Adrienne). All I need to do is take directions and try not to screw up too often. I am essentially a very well paid undergrad! Best thing ever! I should do this more often. I had planned to seriously learn French over the next year because we’ll be living part time in Moorea and because I want to wow the future crew with my language prowess on the next Tara cruise. But maybe I should say !@#$% it. If I don’t learn French, I will be back in the same place next year with zippo responsibilities. Tough choice.

Nico goes up

Two heads aren’t always better than one

But all blessings sometimes are a curse, and sadly there are times when my reticence to speak up ended up biting me in the ass, or in this case, hitting me in the head. I suspect you all know where this is going. Becky gets hurt again. Yep that’s right people. Yesterday, when our new boat driver (name omitted to protect the guilty) decided that the best way to travel, no matter the weather or wave conditions, is at full throttle. On the way out and then again on the way back to Tara my PI brain was screaming inside. “What gives man, slow the hell down.” “Tell him to take it easy, Becky” “Tell him that someone is gonna get hurt and that it’s better to get there slowly than not at all.” But then I look around and eyeball everyone else getting ragged dolled on the boat and they all seem just fine with it. So then I feel like the old lady, tisk tisk tisk. “Slow down, sonny!”  But, alas, I should have trusted my instincts and wagged my finger and made a stink. Instead I now have a shiner on my left eye to match the bruise (which now everyone agrees looks like an atoll) on my leg.

To make a long story long, we went over the top of a particularly large wave at the speed of light. We then landed very hard in the next wave’s trough. Monche (our normal mellow and sane boat driver and DSO) and I both got thrown head first into the bow (we both managed to stay mostly upright and holding on to the side lines). With terrible timing and placement our heads found themselves in the same place at the same time. So I guess that ‘someone’ ‘who was gonna get hurt”… that was me…also Monche. Joy. To be honest I was more pist off than hurt. In fact, even though everyone saw it, and the DSO was asking me if I was okay the driver didn’t even stop. I had to tell him to stop to make sure I wasn’t bleeding or had a concussion. Luckily the wet and hot I felt on my face wasn’t blood, just seawater and pure rage. I’d say it was the first time this whole trip I was actually angry at someone. When we got back, we found that the gash on the right side of my left eye I received from Monche’s noggin was quite minor and was only a small impact cut. My sunglass took a majority of the of the force away from my eye socket and cracked. Monche is bald, and like sailor feet, he has sailor head, a sunburnt nugget covered in bruises and cuts from hitting his head on stuff all the time. So the new lump he got was a nice addition to the rest, and we have officially bonded, perhaps too literally. In the end I got a nasty head ache and a small black eye as well as vindication that although most of the time it’s good to keep your mouth closed… in this case I should have said something. Damn you, hindsight!





Me Kudos and Wanna Whale


Arrived into Gambier yesterday, and it’s been busy busy since then. If Ducie was a postcard atoll this place is the poster child for French Polynesia. Amazing azure waters in between huge mountains of volcanic rock with sheer cliffs. Palm trees and white sand beaches. I’m currently eating coconut harvested from the local beach. My roommate Elsa decorated the back deck with palm leaves, and we are all currently festooned in our tropical wear. Hello, Jimmy Buffett dreamscape. Except sadly no margaritas. God I really need a drink.


Yin and Yang reefs and the MMM

So while the above water sites of Gambier are astonishingly good looking, what about the underwater ones? Hmmm well that’s tough. Yesterday’s reef was, as Pete described, “all sorts of bad.” While there was a lot of diversity and good 3D structure, the corals were mostly dead, bleached, diseased, and in the process of dying. Even the evil fire coral was sick and mostly dead. If one was to stick their head underwater and then above it three times in a row it would sound something like “ugh,” “oh!”; “yuck”, “ahh!”; “eeek” and “sigh!”  Yeah I know that’s a weird thought, but I thought it.

But today’s dive was a very different story. This site was on the outside of the barrier reef and the corals were the healthiest we’ve seen on this expedition.  Plus, it was right at the edge of very deep water, so we were in some amazing fish company: huge schools of blue, pink, and marron parrotfishes (Scaridasomething) along with monstrous unicorn fish and surgeon fish. We were also blessed with several pelagic animals including three different kinds of tuna, giant trevally, and several sharks. It was awesome! Plus, it was a scouting dive so we could just look and watch. The down side of this site, is that it did take us almost an hour dingy ride to get there but I thought ‘hey no worries, it’s prime whale watching time.” Right? But any whales? No. Apparently there isn’t a single freaking whale in the entire Southern Hemisphere right now. I mean seriously, ocean, we’ve travelled 1700 miles, and you can’t put out 1 goddamn measly marine mammal? Sorry about the goddamn, Mom, I know how you hate that, but SERIOUSLY! JUST ONE! Come on! I’m not asking for a whole pod of breaching blue whales (although that would be nice). A dolphin maybe? Porpoise please? Seal sir? Walrus? ANYTHING? No… well fine. Be that way. Keep your whales to yourself. See if I care…. Okay I care, and I’m gonna be pist if I traveled half way across the planet on a sailboat and didn’t see even a whale spout.


I am a marine biologist goddess, beotches!

From some of my posts you might think I am pretty clumsy (true), that I spell bad (totaly true), and that I’m a somewhat of an incompetent marine biologist (incontrovertibly true). But as I think back on the last three weeks I want to present some evidence to the contrary and highlight some of my prouder moments during this sailing adventure…moments where I totally nodded my head, put my hair behind my ears, pat myself on the back, and thought to myself… ‘dude you just rocked that! You are a kickass marine biologist.’ So the following are just a few snippets of random things that have occurred where I owned it.

1. Pencil meets a sharp ‘end’!

When Emilie (me dive buddy) and I were diving one day our handy-dandy pencil’s ‘end’ met a sad ‘end’ (see what I did there…snort laugh) against a rock. Emilie was distressed, but I looked her in the eyes, wagged my finger, pointed to her knife, and sharpened the shit out of that pencil, old school style. Both Pete and Emilie remarked on my quick cleverness underwater. +1 marine biologist point.

2. Tied some wicked knots!

Had to attach some weights to my fancy PVC gear and tied some killer knots I learned rock climbing. When one sailor came by and asked to make sure I did it right, his shocked face at my ropey awesomeness was priceless. +1

3. Taught French sailor guys to speak California girl.

Nothing is more fun than teaching Frenchie sailors weird surfer slang like “cashed” “dude” and “wicked”. Now all the sailors say in a french accent (imagine an accordion is playing in the background) “it is as, Becky, says….casssshhhed” as in “my tank is cashed” “I am cashed” and “the soap is totally way cashed…dude.” No points but hysterical.

4. Only used 200 bar during a 70 minute dive! +1

5. Used my emergency responder training. 

‘Annie, Annie, (really Emilie, Emilie) are you okay? No? Did the first mate smash your fingers under a scuba tank? Yes? Okay, I am, sort of, maybe, trained in first aid. Can I assist you? … and I make the most amazing finger splint ever! +2 points

6. Giant stride off a 103ft sailboat, 15 feet off the deck.

Perfect 10! Threw a “wheee” into it. +1, although the DSO just hung and shook his head. ‘A-mer-i-cans! What show offs.’

7. Can now identify a total of 3 coral species (well, genera really), sometimes. YES! +3

8. Peed in my wetsuit. And admitted it. +1

Even though I was informed that it was not allowed because we wear ‘communal’ Tara wetsuits, I peed in that baby. Many times. You really expect me to go three hours without peeing after I drank five BOWLS of coffee this morning? Right. All you people lie. I know you peed in there. What, the French have giant bladders of steel? I don’t think so. Fess up.

9. Informed the crew that the English name for that bird we just saw is a “boobie.” Lots more snort laughs. +1

10. Gave a fish a kiss.

Remember those annoyingly friendly fish? Well while we waited at a 3-minute safety stop, I took my reg out and literally gave one a kiss. +1, although he/she didn’t like it and swam away. -1

Till next time land ‘lubbers!  -Becky

Living on Sponge Cake, Watching the Sun Bake, The Deck is all Covered in Oil

You know you are procrastinating writing that paper when you spend a good two hours making mix tapes… yes, I know they are called ‘play lists’ now, kids. But this week while steaming to Mangareva I did just that, made three play lists for the crew. I did this because for the last few days I’ve done some unofficial DJing in club Tara. But as to be expected my POS laptop has been acting weird and would only play music in iTunes format and refused to connect to my external hard drive for some unknown reason, so I was limited in my selection of appropriate music for this international audience. But when I finally fixed those issues I had at my disposal 50Gig of sonic bliss. Now we are ready for everything: a euro-style dance party, a chronic mellow chill session, a tropical breezy feel good jaunt, or classic rock sing along festival. With the traverse, it’s nice to just laze around the galley or back deck of the boat and listen to some tunes ’cause reading and writing can induce the heaving (see second half of this blog).

BIRDS! And the Shark Hallows

Oh, I forgot to catch you all up on the sharks at Ducie. Recap! So we did end up seeing a ton of sharks, but really only in the lagoon of the island. A super scary amount as previously predicted. To get to the lagoon we had to traverse the island and literally step over a baby Murphy’s petrel every 3 feet. I’ve never seen so many birds before; it was a veritable bird mine field. Someone described it as a real life video game where you had to step in the right spot or lose a life. It was pretty crazy, and every chick seemed to think we were gonna give him food cause when we got near they opened their beaks and squawked at us, “raaaaaaaa!” I got’s nothing but love baby bird.

Petrel baby

Baby Murphy’s petrel

When we got to the lagoon things got even more wildlife crazy. We suited up and stepped in the lovely blue and green lagoon. (Cross off that digital camera from the list cause apparently even though it said it was water proof, it wasn’t.) The lagoon had two parts, a very shallow (1/2 m) step made out of compressed and fossilized coral bits that was about 100 meters wide. It looked and felt like someone took a gazillion pounds of Acropora branches and melted them together to make a rip rap beach. The water was clear and blue, beautiful and welcoming. Then there was the lagoon itself, a different beast altogether. The edge of shallow area dropped off into deeper and darker water that had a menacing feel. And the place was pretty darn creepy, dark green water with tall 5m pillars of coral that formed a maze. Shark maze! That’s a maze I did not want to go in. If the outside was an advertisement for the loveliness of tropics then the inside was like an advertisement for a bad B-horror movie. Perhaps I felt this way because within seconds (I am not exaggerating) we were quickly ‘approached’ by 12 grey reef sharks. Big fatty sharks, not those little pups we saw on the forereefs. Mama and dada sharks, 2 meters in length and girthy. And when I said ‘approached’ I really meant they swam straight at us, like a pack of either a) happy puppies (preferable really) or alternatively angry pit bulls. Now it’s hard to read the face of a reef shark, but based on their twitchy swimming I decided it was the later and hid behind Chris. Actually all three of us quickly retreated back to the shallows where the sharks didn’t seem to want to enter but from where we could watch them swim around and around. It was an intense experience. After the sharks patrolled the entrance to the lagoon for a good 3-5 minutes they retreated back into the depths where we couldn’t see them and to where we didn’t really want to follow. My impression of the whole things was that the sharks were telling us… “No no no people… I don’t think so. This place is ours, so STHO.” So we did. While I cowered at the edge of the lagoon, I nicknamed the place the “shark hallows.”


On the way back to the ship I got to see even more sharks. I saw more sharks in that 2-hour trip than the rest of the trip combined. As we snorkeled through the remarkably beautiful shallow reef adjacent to the boat we saw a tons of huge monstrous lobsters and 3-4 sleeping white tip sharks. I actually think it was one of the prettiest sites I saw on the island, although it’s hard to be a tourist when you are working underwater. But as I swam from the reef over to the deeper water where the ship was anchored, I saw a small baby white tip (1.5ft maybe) take off from the bottom and high tail it towards me. Now a shark is a shark no matter how small, but I was only a little concerned ’cause this thing was so little. Well at first. But this shark was making a bee line to me like you couldn’t imagine, and I thought “what the hell does this baby shark want from me?” A hunk of flesh? Or a cuddle? Well I picked up some speed and grabbed Chris who’s more than 6ft tall and 230, showed him the shark, and hid behind him again. He makes a conveniently large barrier. When we both faced it, it sort-of slowed down, but it was still heading straight for us, like it was on a mission. Then another person came over and the shark finally changed its mind. It turned and started to circle us. We swam around each other for a while and I started to realize this animal just really wanted to check us out. It was curious beastie! We were probably the first humans it had ever seen and it, like any kid, wanted to play. Or least I hope that’s what it wanted. But it was an experience that really stuck with me. I can imagine that shark’s face in my mind’s eye very clearly, and I sincerely hope that he/she gets to live a nice long sharky life at Ducie. I thought it was a very appropriate last water experience at Ducie Island, and it left me with a good feeling instead of the sadness I experienced on the first few dives. Thanks, little buddy.

Homesick Seasick Mesick

After we left Ducie we started our 4 ½ day journey to Mangareva. When we are underway this is usually when people suffer from seasickness. Luckily thus far I have had only three minor bouts of seasickness. One with the blue cheese pasta in the big seas and the other when we weren’t really moving at all, but when someone showed a shakey handcam video reel of sharks in the lagoon. It was Blair Witch yackatude all over again. Although to be honest, I haven’t actually spewed chunks at all this trip.  Just wanted to really. And then there was yesterday. Since we collected the bleaching data at Ducie the other scientists and I have been very motivated to wrap up our analysis and write a paper. The bleaching we recorded was around 30% and the more coral there was the less bleaching. So while I attempted to make some Excel graphs I got super motion sick. Now Excel graphs usually just make me metaphorically sick, but in this case they made me literally sick. Haven’t really recovered yet, and had been feeling pretty horrible all day yesterday and all last night. That’s why this blog is so late in the coming. Also, laying in bed all day can make you feel physically better but unfortunately it’s not good for the soul. Add super homesick to that seasick and you have a sad Becky. I guess its par for the course after three weeks away, but I am really missing my family, friends, and my students right now. I’m having a hard time knowing that its still two more weeks before I am home. In a funny twist, when I was feeling angry at Microcoft and then sick afterwards, my roommate Elsa quipped “it’s actually nice to see you angry and sad, because it shows you are human.” And I was very human yesterday. A tad too human for my taste. So to cheer me up, please send me emails (becky@tara5.oceanbox.net) and tell me what you are up to these days, what you are currently thinking about, or how much you love or hate my blog. Till next time, salty dogs!

Things fall apart

Current position: 24 26 886 S, 125 29 376 W

# miles to Gambier: 529

Wind speed: <15

# of times hit head on hatch today: 0, but made up with it by hitting back of head on a low hanging ceiling. Cried a little.

# of gallons of diesel fumes consumed: 12,583

IQ score: -2

# of completely intact toe nails: 7

Avast me hardies. It’s time to trim the main! Baton down the hatches! Flibber the gibbits! We are off to sail the ocean blue. Actually… don’t do any of those things I just mentioned because there is no wind, and once again we are using the engines to make it on time to our next island, the Polynesian island of Gambier. In truth, its Polynesian name is Managreva and only the French call it Gambier. But I’m sailing with a French crew so I will continue to call it Gambier unapologetically. We left Ducie Island this morning and should reach our destination by the 20th. Then we will have six days to complete our mission on this portion of the Tara Pacific expedition. For today’s longish blog, however, I will recap some of the events and issues of the last few days of work at Ducie.


Ducie got all scienced up

In all regards the past trip to Ducie, it was a remarkable success. We did all the things we aimed to with the exception of collecting a coral core because we couldn’t find any coral heads big enough. Along with the things we aimed to do, the coral team also managed to conduct two additional unplanned projects. Given the remoteness of this location, only a single study has ever been published about it. So we reasoned that since we were here, let’s science the crap out of this place. So we (one microbiologist, one phylogeneticist, one physiologist, and one biogeochemist who doesn’t study corals at all) did it to the best of our abilities. We conducted a coral biodiversity study were we basically took tiny bits of everything we could visual distinguish as a coral and put it in some buffer for genetic and microbiological analyses. We also conducted a bleaching prevalence and severity study. That means this microbiologist got to wear her ‘marine ecologist’ hat, which in this case took the form of a transect tape and stuff made out of PVC with holes drilled in it, duct tape, and zip ties. Definitely zip ties. Can’t forget the zip ties.

So with our quadrats and transect tapes, we did 18 bleaching transects across three sites on the island. And there was a shocking amount of bleaching, although again the reef is insanely beautiful. But to our knowledge, this will be the first report of bleaching in Ducie. And how weird is that? Well one way to tell you how weird that is, is to give you the water temperature I endured for 70 minutes yesterday in my 5mm wetsuit. 19C (66F, ‘Mericans)! I was so cold by the end of that last dive at Ducie I could barely write on my slate. After I got on board and finished all my clean up duties I spent two hours under my goose down comforter to warm up. Shit was Arctic down there.

So if it’s so damn cold here then why are ~100% of the Pocillopora and 50% of the Montipora at 10-15 meters water depth bleached, you ask? Good question, the one person reading this entirely too long blog. In truth, I have no good answer, and we will likely never know. But I suspect it’s because sometime in the recent past is wasn’t so cold and was hot enough to bleach the corals. Now remember kids, this is the Southern hemisphere so its winter now. But in just April there was bleaching in Moorea, also in the Southern hemisphere. But Moorea is also 12 degrees north, while its 24 at Ducie. So much farther south. Nevertheless, perhaps during the summer months it got warmer than the sub-Antarctic waters we experienced this week. And I guess if that was true, then most of the corals have recovered but a few sensitive species have not. Now I am no bleaching expert, so I just don’t know, but that’s what collaborators are for.  So when I get back, I’ll consult with them (Adrienne Correa I’m looking at you). Everyone will have to sit tight on this story until then.

Sailor feet and dishes

Now if you were paying attention, then you’ll note the title of this blog. We are now three weeks into the five week trip and stuff is seriously starting to falling apart. The boat. The gear. People. Everything has a breaking point, and at sea, that point is left of center. Right now every crew member is trying to fix stuff before we get to Gambier ’cause too many serious things can go wrong when stuff falls apart. For example, the first concerning thing to break was the desalination machine. Water. We need it. Not that salty stuff we’re sailing in, but fresh, sweet water. To drink. To cook with. And to clean stuff in. But no desalinator and no fresh water. Luckily we have a crew that can fix almost anything. So now it’s sort of working but showers are short and we clean our dishes in salt water.  

Speaking of dishes. Another thing that seriously inconvenienced our life was the discovery that “we are sinking.”  “Sinking!” At least that is what I was told by the first mate and captain in a very flat tone when I discovered about five people huddled around the galley sink the other day. My reply… “excellent…” and then I went on to finish up my duties. Apparently the kitchen sink hasn’t been flushing into the bilge area but instead into the hull of the ship. So we were taking on water, or we HAD taken on a lot of water. Days’ worth. Days’ worth of sink-water. Think about that for a moment ’cause it’s gonna be important later. But the engineers were back to the rescue. It took them two days to fix it. Unfortunately, one of those days was when I was on dish washing duties.  So I had to haul, and then wash, dishes and cookwear for 16, on the back deck, in the dark, in the rain. Both ways. No me gusta.

Importantly, when I was crouched down in that rain that night, I started to notice a strange phenomenon among the crew that I deemed “sailor feat.” Yes… sailor feet.  As each member of the crew showed up to the back deck with even more dishes, I was in close, intimate proximity to their feet. Thus I started noticing just how jacked the feet of sailors are. They are all sorts of messed up. There are toes pointing the wrong ways. There are lumps and bumps where there should be no lumps or bumps. There are cuts and bruises and scars galore.  I guess it comes with the territory where even the most seemingly innocuous part of the boat is a weapon of mass bodily destruction waiting to happen.

So fast forward a couple days to last night when in reflection, I looked at my feet and thought “yep, sailor feet, here I come.” Cause my feet now look like raw meat.  My whole left foot is mangled. I lost half my big toe nail, cut my little toe down the middle, and my foot is all black and blue half way up to my instep. Oh and did I mention my leg? Well remember that broken sink and the water in the hull? You might have wondered, “how does one get rid of water in the hull?” I thought it would involve some fancy smancy equipment but nope, just a vacuum. Wet/dry vacuum to the rescue. This precise activity was a quite a sight to behold. The engineer deftly held the hose and the first mate expertly turned on the vacuum, and whamo!, a tub full of the most disgusting old sink water from dinners, lunches, and breakfasts past… mixed with oil and grease for maximum disgust. Yummy. After I watched them do this seemingly mindless task I remarkably, stupidly, asked if I could help. I thought I could handle that turning the vacuum part on pretty well and would get super awesome cred for being so helpful. Instead, I was unceremoniously handed said bucket of yuck and told to haul it upstairs and pour it overboard. I looked at the bucket and thought, hmmm, this seems like a more than I was bargaining for… but hell yeah, I can do that! Also I didn’t want to look like a wuss, so time to get that bucket cleaning done.

What then transpired was a lesson in knowing one’s limits but then ignoring them entirely. I did manage to make my way up the stairs of a moving vessel holding in both hands a couple gallons of filth. Got to the top and onto the deck. I thought “that wasn’t so bad. I so got this.” Then for the harder part, I had to traverse the assortment of metal-thingies, ropy-thingies, with no hands to hold onto stuff, and then make it to the edge of the boat to pour bucket of yack out without falling in myself. Sadly, albeit not entirely unexpectedly, I made it only half way and slipped on the rainy wet deck. Me, bucket, and 10 liters of the most impossibly disgusting assortment of mostly rotten human edibles landed on said metal thing. Nailed it!

Lucky for me only one sailor was witness to my shame and sudden filthiness. To make matters worse I had just literally showered and changed into clean clothes which I had just gotten cause the washing machine had been broken for days. But pride being what it is, I said “I’m fine. It’s nothing. I’ll just pour the 300 mL’s left of this bucket over the gunwale and clean up the deck.” After I did, I went sheepishly back to the galley a good ten minutes later to give the bucket back to the first mate without looking him in the face and went and took another shower. So how bad was it?  Well, I didn’t break anything, but see ‘sailor feet.’ And for maximum gore I’ve attached a picture! You’re welcome!

Really, you're welcome.

Really, you’re welcome.

But I’ve had worse. And the whole thing has given me a great excuse to lie around and tell all my horrible injury stories to anyone willing to ask. You all know I love to tell a “once when I was blah blah blah, I got blah blah blah…”. Plus, drop one injury story at dinner with a bunch of people with sailor feet and you’ve got an evening to remember. And since it was our last night in Ducie, we celebrated by having dinner on the deck with some wine and good music to dance and limp to.

The life of a PhD student

I was starting to get a little jealous of Becky and Stephanie writing all the recent posts. So I’ve decided to make my own return to the blogosphere, today, by posting my answers to a few questions sent to me as part of a high school assignment. I enjoyed taking the time to answer them, and think they fairly succinctly summarize what life is really like for me as a grad student. (hint: it’s not all splashing around in the tropics or making grand discoveries).  So, here they are, with some minor additions and corrections:

What does a day of work look like for you?

There isn’t really any ‘average’ day for me – during different times of the year or different stages of a project, I have very different tasks to do. I would guesstimate that I spend 40% of the year analyzing data, 20% doing lab work, 15% preparing for fieldwork, 15% doing fieldwork, and 10% doing other tasks.

Data analysis is huge for me because I work with many terabytes of genetic sequence information, and have to learn and write code in multiple programming languages in order to handle it all. Sifting through that data and finding interesting patterns takes a lot of time! So on those days (which include today), I generally wake up, check the status of scripts that were running overnight, have breakfast, and then go to my office for the rest of the day to do statistics and scripting work on my computer. Veteran readers of this blog might remember the last few posts of mine, where I detailed some light data-wrangling and mapping tasks that were occupying me at the time. Most of my computer work is slightly more dry than even that… But to me, the results of this work can be the most exciting part of the job! And getting scripts to run smoothly and efficiently is an extremely satisfying experience! 

I suppose an average day for me looks something like this.

Before I can do data analysis, though, I have to collect samples and generate the data. Prior to traveling and getting into the water for sample collection, I have to do a lot of paperwork and preparation: gathering supplies, applying for permits and travel visas, arranging housing and transportation, establishing on-site emergency procedures, brushing up on my SCUBA and first-aid skills, and researching what kinds of corals I expect to find and collect at each location. A lot of this is by far my least favorite part of the job, and is a major reason that I’m feeling a bit burnt-out from fieldwork, lately! Paperwork and bureaucracy were not what I signed up for! But following the law and being safe are extremely important, so I spend a lot of time trying to make sure I do everything right when I travel.

Acquiring permits is my favorite part of the job... Wait, no, that's not quite right...

Acquiring permits is my favorite part of the job… Wait, no, that’s not quite right…

Of course, the most fun portion of my work is the fieldwork itself! There’s no point in describing that here when you can instead watch this video: https://youtu.be/whQTKjexHCw. Again, veteran readers of this blog will also know what fieldwork is like for me from my previous posts and photos.

Ahh, that's right, diving is the most fun part of my job!

Ahh, that’s right, diving is the most fun part of my job!

After collecting samples in the field, I have to process those samples in the lab here in Oregon. I often say my lab work consists mostly of moving clear liquids from one tube to another – extracting, cleaning, aliquoting, and amplifying DNA, enzymes, and other colorless chemicals. It’s the kind of work that becomes rather mindless once you’re experienced, and can sometimes serve as a good time to get lost in thought. Ultimately, the result of all my liquid-mixing gets placed in a DNA sequencing machine, which spits out the aforementioned terabytes of data for analysis.

Moving liquids around in prettily-colored tubes isn’t so bad, either, though…

Why did you choose to become a marine biologist?

I had a pretty good idea that I wanted to be a scientist of some sort for as long as I can remember. I’ve also always been in love with tropical ecosystems, for some reason that I can’t explain. I think I decided more specifically on biology gradually throughout high school, during which I had a couple of important experiences. I remember in Sophomore biology class being fascinated by the workings of the cell; how diverse proteins are and how they act like such perfect miniature robots. My AP Biology course during my Junior year was exciting and incredible to me for all sorts of reasons. And between my Junior and Senior years, I worked as an assistant in a pathogen genetics laboratory here at OSU, which kind of sealed the deal for me. Choosing marine biology was a somewhat spontaneous decision that I made when I was applying for college… I don’t actually know why, but at some point during that process, I just decided that that was the program I was looking for. It probably had something to do with having had 5 fish tanks as a kid, playing water polo and swim team, and having loved learning to SCUBA dive on a family vacation to Hawaii. I just loved being in the water and seeing the beautiful and strange animals that inhabit it. Then, after I had started studying it, I realized just how amazing life in the ocean really is, and there really wasn’t any going back!

What are challenges you face in your studies/at work?

I think right now my biggest challenge is the communication of my work to my fellow scientists and the public. That communication is really the most important part of a scientist’s work; we get paid by publicly-funded grants so that we help everyone gain a better understanding of the world around us. Our primary mode of communication is through the publication of peer-reviewed manuscripts, and right now, I have a lot of discoveries that I need to share, that I’m struggling to write about. Part of that struggle is due to some perfectionism: nothing in science is ever 100% proven, and I always want to find better evidence and consider every possible alternative before declaring to the world that something is true in a publication. But at some point, I will need to write things up according to my current understanding, while simply acknowledging that parts of that understanding are bound to change.

This blog is another important form of communication for me, because I get to speak more freely to the public. But communicating our science to the public is also a major challenge. A lot of people want to live vicariously and hear about the fun parts of my job, but if that’s all I ever talk about, other people start to wonder whether my job is worth the tax money. So I try hard in my posts to blend fun stories with useful educational material, and it’s not at all easy for me.

Do you work more in a lab setting or out in the ocean?

As per question 1, the majority of my work is not out on the ocean. But a significant fraction of it has been! As my project progresses, I will be spending less time on the water, but I’m really not complaining at this point. It’s a lot of fun, but it’s exhausting and disruptive to my career and personal life. 

What is your favorite part about being a marine biologist?

I really like to think that my work can somehow contribute to a better understanding of the world. Coral reefs in particular are in a real mess at the moment, facing threats from pollution, overfishing, climate change, etc., and I want to do what I can to learn about them, and maybe even help them, before they’re gone. Of course, experiencing them in-person during fieldwork is also amazing!

If you are more curious, check out a summary of my work here: http://oregonstate.edu/microbiology/vegathurberlab/global-coral-microbiome-project, and also the videos that we’ve been producing during that project, here: http://marinestudies.oregonstate.edu/global-coral-microbiome-project/.

Thanks for the questions, Sophia!