Indy Sea

Marine Biology grad student, part-time blogger, and vagabond. Likes invertebrates.

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Copepod in Pond Water, captured by Mark Smith and Annette Evans from Macroscopic Solutions.

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A little bit of science doodling – I mean, illustration – for outreach.

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Time lapse of us kayaking to Cherry Cove!

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Not-Automatic Out of the Office Update:

Hello from Catalina!

My assistant, Kelly, and I have been here on Catalina for a week and a half. We're right in the thick of what biologists would call "field season", although that's a loose term. "Field season" often coincides with spring/summer but it's actually whenever conditions are good for going out in the field to do what you need to do. For me, fortunately, it's a sunny Southern California summer.

I've been working all summer on collecting data for my thesis. Mostly this has been a lot of laboratory trials on campus with the occasional collecting trip to local beaches to get my Bertie Bott's Every Flavour urchins. Reds, purples, crowned urchins... Anything I can find.

But right now I'm out at the Wrigley station on Catalina to do some environmental light measurements to complement my lab trials. It's been a lot of diving, a little bit of collecting, and a fair amount of lab trials. The freedom of planning and executing my own work is simultaneously terrifying and exciting. Kelly is my indispensible extra pair of hands and dive buddy, and is definitely less scared of the bison on the island than I am.

Life on the island moves at its own pace, and it's hard to believe we're just 29 miles off the coast of Los Angeles/Long Beach, the busiest port on the west coast. Although there's a basic rhythm to the day based on mealtimes at the lab cafeteria (do not be late or you will be hungry), our schedule out here is all over the place. Need to collect animals but low tide is 7am? We're up at 5:45 for a dawn dive. The full moon is the first weekend we're here? Night dives at 12 and 1am it is. It definitely led to a few interesting Friday night texts to friends back on the mainland.

me: sorry, gotta go now. need to get ready for a dive friend: but it's like 12:30am me: yeah i know. it's a full moon, gotta get those data

It's been hot on land lately but we're in the water so much we've hardly noticed. Sea surface temperatures here have been abnormally warm the past few years, and this summer is no exception. Although it's gotten down to 18ºC (66ºF) at depth, it's been 21-24ºC (70-75ºF) at the surface even at night. The major effect of this is that there is no kelp out here, since giant kelp (Macrocystis sp.) has an upper thermal limit of around 22ºC (71-72ºF). No kelp means a less diverse reef system, fewer fish, and slightly less awesome diving. On a positive note, warmer temperatures means visibility is better and that we can wear a little insulation less while diving. I've been diving without my hood and gloves and it's frankly a relief to not feel completely encased in neoprene, with just a tiny window for my smushed face.

Most days we dive at least once, which has to be scheduled based on the conditions we're trying to sample (noon, sunset, full moon, etc.) and with consideration for the tides and the weather. In between time is filled with data entry, aquarium maintenance, and running more lab trials. Diving is fun, but it's a lot more fun when you don't have lug a heavy bucket of urchins uphill to the lab building afterwards and enter data. After diving all I usually want to do is eat a big meal and take a nap.

I wouldn't say we're not having fun... but I wouldn't exactly describe it as fun, either. It is great being out in the water a lot. There's a lot to see and the conditions while we've been here have been just about idyllic. To the non-scientists out there, I would describe it as hard work that is rewarding. It's a good time, but it's still hard work.

So, I'm not complaining. I just wear a lot of sunscreen, eat a lot of food, try to nap soundly when I can, and keep wondering how and why tiny random cuts keep showing up on my hands.

Better than tell you more, I'll show you what we've been up to. Click on the pics above to read more.

Kelly exploring and chasing some juvenile blacksmith. 

Adorable pelagic red crab (Pleuroncodes planipes) at Two Harbors. A bunch of these guys washed up last weekend, carried up from Mexico by a surge of warmer waters.

The sunsets here are pretty incredible.

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Barnacle ciprid larva sketch from plankton samples

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Cool time lapse of our anemone, Anthopleura elegantissima, feeding on some brine shrimp (Artemia).

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A couple cool guys from the lab recently: sand castle worms aka honeycomb worms (Phragmatopoma sp.) and some polyps of the California gorgonian (Muricea californica).

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[S]tudying only what’s at the bottom of the trench is like studying a mountain by examining only what you find at the summit.

“World’s Deepest Fish” Uses Physiology to Withstand Pressure Originally posted 1/14/15 on the UCLA EEB Facebook Page A new species of snailfish was found at nearly 28,000 ft. below sea level, where the pressure is an astounding 1,000 atmospheres, making it the deepest bony fish ever found. At that depth, the squeeze of the water pressure isn’t just on the fish’s skeleton and muscles, but on its cells and proteins as well. To hold up at a molecular level this snailfish uses a compound called TMAO (or Trimethylamine oxide). (Side note, the fish hasn’t yet been named since it was only caught on video; a specimen must be collected for a full species description to be made.) TMAO is used by many fish to stabilize proteins and prevent them from denaturing (aka losing their 3-D structure). Proteins are vulnerable to denaturation from chemical or physical pressures. Many fish use TMAO to keep proteins from being denatured by nitrogenous wastes. Elasmobranchs (sharks, skates, and other cartilaginous fishes) in particular use this as a strategy to maintain high urea concentrations balanced by TMAO to sustain an internal osmotic concentration roughly equal to that of the seawater that surrounds them. However, some families of deep-sea bony fishes use TMAO to keep the intense water pressure from physically forcing their proteins out of shape. Discovery of the fish came as part of an ongoing effort to explore not just the bottom, but the unique environment found in descending the Mariana Trench. From the article: “As co-chief scientist Jeff Drazen said, studying only what’s at the bottom of the trench is like studying a mountain by examining only what you find at the summit.” Read the full story:  Deepest Fish Features Angel Wings, Tentacles and Amazing Ability to Perform Under Pressure [Scientific American]

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This month I've been selected be the guest editor for my department's Facebook page and imbue it with the theme of Physiology. I do, after all, study comparative physiology to an extent. My thesis will be about sea urchin photosensitivity and visual abilities and so you could categorize what I study under several broader or narrower umbrellas: visual ecology, behavioral ecology, sensory biology, ecological physiology, or comparative physiology. That's far too many labels for me. 

Anyway, that's not the point of all of this. I'll be posting throughout the rest of January on the UCLA Ecology and Environmental Biology Facebook page about interesting physiological phenomena. Check back frequently or like the page on Facebook to get all the stories!

My first post, below. (Original link here.)

Welcome to the January of Physiology Posted by Julia Notar, EEB Guest Editor

Hello there! My name is Julia and I’m a first year master’s student studying comparative physiology. Specifically, I am looking at sea urchin visual ecology, or how sea urchins use light to navigate their environments. No, sea urchins don’t have eyes, but they do react quickly to light and dark! My goal is to find out how much light they need to navigate and whether this ability is influenced by the depth at which a species lives. I’ve added a few pictures, so you can see what I do in the field and lab!

I find physiology really fascinating because it's all about what you can't see. It's all the hidden processes that are going on inside an animal all the time, the way our cells are metabolizing our breakfasts right now without us even thinking about it.

It's also about putting yourself in the shoes (so to speak) of another creature. What is it like to see like a mantis shrimp? How thirsty do you get if you're a camel? How cold is too cold if you're an Arctic fish? If a whale sings at the wrong frequency, can other the whales understand it?

Every environment poses different physiological challenges to its inhabitants. Sometimes we, as scientists, are good at predicting what those challenges might be and how animals might "solve" them. Other times it's a total surprise, which is the best of all.

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Great cartoon by Kate Beaton who draws Hark! A Vagrant. Her explanation of the comic: 

Every Lady Scientist Who Ever Did Anything (until recently).  The trouble with reading about a given woman's history who was born before your mom is that sometimes, they were hilarious, powerful, tough, loud, et cetera et cetera all good comic making material! But then sometimes, man, the main thing about them is that they just got screwed, big time. I think when I read about Rosalind Franklin, or Mary Anning, or whoever, of just how shitty stealing someone else's ideas really is. If I opened a newspaper and saw my comic in it signed by some random dude who was getting paid for it, I'd lose my cool! Dear readers, I would have an undignified tantrum. Wouldn't you? 

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Why so many pre-meds?

As a teaching assistant, part of what I love doing is talking to my students about their career goals. Some of them know what they want to do, many of them don't, and a handful are pretty skilled at telling me what they think I want to hear. A large proportion are pre-med or pre-health. This question is posed at the end of a thoughtful article on School of Doubt on advising students about career options:

"Here’s my question to you: what makes students so intent on specific career options so early?"

In other words, why do so many of our students want to become doctors? The article is good and wonders why pre-med is such a popular major among life sciences majors. The author floats a couple of hypotheses, including the hero complex and prestige of the position.

While I agree, a couple of other factors I didn't see mentioned are family pressure and the fact that the road to becoming a doctor is quite standardized. I'm going to set aside family pressure for now, which can be a very strong and complicated factor for many students, as it really warrants an entire post (or book) of its own. I think this second factor, the desire for a set pathway, is more common than we realize. Let's be honest: very few jobs out there have linear career paths leading to them. Sure, pretty much any profession requires that you bring certain skills, experiences, and maybe a degree or certification to it, but a majority of people out there didn't get to their current job by traveling in a straight line. Not even (or especially) the academics I work with now. An example, from Duke professor Sönke Johnsen:

I entered college and quickly discovered that my Physics classes bored me. I switched majors to Math, mostly because my favorite teacher at the time — who shared my interest in modern dance and told funny stories about Abel and Galois — taught this subject. This major also gave me time to do what I really enjoyed: dancing, painting, playing practical jokes, and worrying about my personal life. I graduated early, moved to a clothing-optional group house with my girlfriend, and started teaching dance to three-year-olds. I fully expected to never return to academia.

(I highly recommend reading the rest of his fantastic Q&A for the full story.)

Given that most people land their jobs by some mixture of circumstances, geography, opportunity and luck, momentary personal motivations, and 'just figuring it out', becoming a doctor (or planning to become a doctor) is reassuring in this sense. There are on the order of 10 years' worth of hoops of definite heights to jump through. A close friend of mine who recently became an RN told me of the pride she felt in her achievement: "I set myself a goal, I went through all the necessary steps, and here I am."

To become a doctor you know exactly what you have to do: get good grades, do well on the MCAT, go to medical school, do your rotations, complete a residency, and then, BAM, DOCTOR. For a directionless college student (there are many and I was one) a proscribed pathway can be reassuring. It is much less comforting to hear, "You'll figure something out, but first you have to go wander and struggle and be a bit lost until you do." I had a wonderful Albanian math teacher in middle school who was fond of telling us, "Freedom is like a fat in your body."

This linear pathway is not unique to doctors, and includes many of the health-related professions, lawyers, and others. As a graduate student in the life sciences, I think we tend to see the most wanna-be doctors because biology is the most obvious plinth upon which modern medicine sits (and at a university like mine where there is no official pre-med major the biology-related majors are packed with pre-meds). Additionally, compared with other health-related professions, "medical doctor" carries with it the one-two of high prestige and high earnings. My students' backup plans are usually quietly considering pharmacy school, PAing, or dentistry.

The article asks a second question at the end: "How do we expose them to what [their early, restrictive career fixations] will really mean?" For that, I think the best thing is to encourage students to engage in volunteering and internships in their desired field early. They should seek out (and we should help them find, as much as possible) older students and professionals in the field to talk to. This would help them think about their career path more critically and expose them to the realities of what it means to be a doctor (and more than the melodrama, hero worship, and martyr complexes portrayed on House, Grey's Anatomy, and other TV shows).

What do you think? Anything else we're missing? 

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Great cartoon from XKCD. This is why I do science! Where DO birds go when it rains? It is really cool how some questions are near universal. Some things we have answers for, some things we don't. There's a thrill and satisfaction in finding the answer in a book or article; it's even more exciting (to me, anyway) when you realize that we don't know the answer yet. 

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Bye for now, LA. I'm off to do a little teaching and a little research!

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"[T]hough our knowledge increased our ignorance was scarcely diminished." I love that bit and the paragraph that follows. From D’Arcy Wentworth Thomas’ introduction to Nomogenesis by Leo S. Berg. 1926.

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Statistics is a like a bikini bathing suit, what it reveals is interesting, but what is conceals is essential.

Dr. Malcolm Gordon Quote of the day on my students' blog! Check out their adventures as they do their research projects out at Catalina: MBQ 2014.

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There are two possible outcomes: If the result confirms the hypothesis, then you've made a measurement. If the result is contrary to the hypothesis, then you've made a discovery.

Enrico Fermi, physicist and Nobel laureate (1901-1954) 

via A.Word.a.Day

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Great article from The Scientist about a new wave of science communication contests sweeping academia. From Three Minute Thesis (3MT) to FameLab...

Contests that challenge young scientists to explain their research without jargon are turning science communication into a competitive sport. Early on, organizers of such science communication competitions say they faced skepticism from faculty, many of whom were concerned that a contest would denigrate serious research. But CIRM’s McCormack refutes the idea that making science easier to digest cheapens it in any way. “Just because you’re simplifying it doesn’t mean you’re dumbing it down,” he says. “You’re just making it accessible. I don’t think it trivializes it at all. In fact, in many ways, I think it raises it.”

I completely agree. Explaining science in a straightforward, accessible fashion doesn't necessitate dumbing it down. TED Talks are an excellent example of this. The presenters bring complex topics to curious audiences in engaging ways and their popularity is a testament to the success of such a format. More and better science communication can only serve to benefit both science and the public.