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 pictures for captions.)

“World’s Deepest Fish” Uses Physiology to Withstand Pressure

Originally published 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]

January is for Physiology!

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. (Originally published 1/13/15.)

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.

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?

Lionfish or honest fish?

[Originally published July 31, 2014]
Last week’s buzzworthy ecology story about 6th grader who ‘discovered’ euryhaline* lionfish leaves everyone pointing fingers

The full context surrounding the story of a sixth grader’s science fair project sticking it to The Man (if The Man is native estuarine of flora and fauna) is finally coming to light. The coverage of Lauren Arrington’s project, which demonstrated that lionfish can live in low salinities, has left a messy trail of missing credit and hurt feelings in its wake. My only hope is that everyone who enthusiastically shared the initial story will get to read the follow up.

To fill you in on the backstory:

Arrington’s experiment revealed that lionfish — the invasive, venomous species of fish thought to be native to saltwater oceans – could actually survive in nearly freshwater environments, which could potentially damage the marine ecology of estuaries, where salty ocean water and fresh river water mix.

The story went viral. Arrington’s work was featured in science magazines and local newspapers, and word of her “breakthrough” discovery made its way to major news organizations, including NPR, CBS and NBC.

But on Monday, a marine biologist by the name of Zack Jud made an explosive claim: All these stories were based on a “lie,” because Arrington was taking credit for research he’d published three years earlier. [WaPo]

As the Washington Post states, the story exploded. Everything is there to make the internet collectively squee: precocious youngster, saving the planet, and rocking The Establisment’s boat (if The Establishment is Marine Ecology).  NPR originally covered the story thusly, though they’ve since updated the piece:

Unfortunately, on the internet headlines travel faster than facts and the speed of propagation of a tweet is proportional to the inverse of its veracity.**

I’m not going to take sides here (those who are interested in doing so should read the full Washington Post article, this io9 piece, and Dr. Craig Layman’s timeline of events) as I want to make a different point. This whole kerfuffle underscores the importance of having highly science-literate journalists. Those who write about science need to thoroughly understand how science works, as a field and a process. Just as in marketing, law, or any other profession, science has its own shibboleths and rules of collegial conduct.

As a scientist you have to cite who you worked with and where your ideas came from (if not all your own, which they rarely are). This isn’t just important, this is tantamount. It isn’t like award shows where you can get up there and thank your mom and Jesus and all the little people when you and your PA both know you wouldn’t be there if they didn’t drag you out of bed every morning and have that almond milk half-caff no foam latte to get your brain started.

My speculation (and I want to stress, this is only speculation) is that the proper credit was lost at an early stage, between subject and journalist, or original article and viral reposting. A non-scientist could easily interpret a comment like, ‘She got the idea for her project from my colleague, Dr. X’ as an offhand remark instead of a crucial piece of the story. With the wheels of the internet news machine spinning as fast as they do in our modern world, flawed stories get shared (at best) and loosely paraphrased as new posts (at worst) faster than you can say “fish fight”.

All of this underscores the deep irony that we simultaneously live in an age where we have to fight for our right to be forgotten on the internet but nobody fact checks anything anyway. It took me all of 2 minutes to search Google Scholar for pre-2012 papers with “lionfish low salinity” (Jud’s 2011 paper is the second result) and find that Arrington did in fact cite Jud when she published her results in 2012.

Fact check your stories, people. Do it for the kids. (And adults and dogs and everyone else who uses the internet).

*Able to survive conditions across a wide range of salinities (e.g. from seawater to freshwater)

**It may be helpful to think of tweets as having the properties of both waves and particles.

Science Speak [The Scientist]

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.

Variations on a Theme

Via deepseafauna with googly eyes:

Do you prefer the biologically accurate googly-eyes at the terminus of each arm…


…or the more whimsical pareidoliaic face?


Hippasteria spinosa.

[Photo by Ed Bowlby, WoRDSS.]

I, personally, am going to have to go with biologically accurate, although I do think googly eyes improve anything and everything.

But wait, you say, hold the phone. I can see that sea stars don’t have two eyes in the middle — “Correct!” I interject — but they definitely don’t have eyes on the ends of their… legs? Arms? What are those? (Arms.)

Ah, well, how am I going to put this. It turns out, sea stars actually do have eyes there. Tiny, structures that hold clusters of light-sensitive photoreceptors sit at the end of each arm, giving sea stars some rudimentary vision.

It begs the question, however, why would a sea star need to see? They’re not exactly speedy, so the sight of a predator swimming straight at them won’t send them racing away. (They’re not cartwheelingspiders, after all.) While the exact behavioral use of their eyes is still open to speculation, it’s quite likely they use their vision for rudimentary navigation.

A recent study looking at the vision and behavior of sea stars supports this hypothesis. Published in the Proceedings of the Royal Society B earlier this year, the study investigated the small-scale navigation and the eye function and physiology of the blue sea star, Linckia laevigata, a tropical species that makes its home on coral reefs.


[Linckia laevigata, from the California Academy of Sciences Research Archive]

In addition to exploring their eyes’ spectral sensitivity and resolution, the researchers, Anders Garm from the University of Copenhagen and Dan-Eric Nilsson from Lund University, found that normal Linckia sea stars were able to navigate back to the reef when placed up to 2 meters away, while experimentally blinded starfish were unable to find their way back. Pretty stunning for an animal with no advanced eyes and a simple nervous system.

This new information just adds to the fray that is our understanding of echinoderm vision. Echinoderms, an invertebrate phylum closely related to vertebrates, include sea urchins, brittle stars, basket stars, feather stars, crinoids, sea cucumbers, and our noble, sighted sea stars. Though several of these animals sport rudimentary vision and the odd pair of rogue googly eyes, none of them have eyes nearly as advanced as vertebrates. Still, as close invertebrate relatives, the development of echinoderm eyes may hold some clues for the development and evolution of our own.

App set to map the oceans’ plankton [BBC News]

Spend a lot of time out on the water and interested in getting involved in some citizen science? You can help marine scientists track global phytoplankton productivity… with your phone.

Marine biologists have been using the Secchi disk method to measure the abundance of phytoplankton for 150 years.

The white disk measures 30cm (1ft) in diameter and is lowered into the water on the end of a tape measure. When it is no longer visible from the surface, the reading – known as the Secchi depth – is recorded.

“It is a very robust method and not prone to error and it is a good measure of phytoplankton abundance,” Dr Kirby told BBC News.

“Away from estuaries and more than a kilometre from the coast, the main influence on water clarity is phytoplankton.”

He explained how he had the idea of setting up a citizen science project: “It occurred to me sat at my desk that while there are a lot of scientists, there are not that many that are marine scientists, and fewer still that go to sea.

“And the ones that do go to sea do not go out very far. If they do go out far, they rarely go back to the same place.

“I thought that there are an awful lot of sailors out there; day sailors, cruising sailors. Many of these sailors will sail the same waters and take the same route time and time again.”

The full article tells you how to get involved and provides this interesting, surprisingly Papal history of the Secchi Disk:

The Secchi disk, invented in 1865 by Angelo Secchi – the Pope’s astronomer – is a circular disk that is used to measure water transparency in oceans and lakes.

The concept had long been used as a navigational tool by sailors. By lowering a dinner plate beneath the waves and measuring the depth it disappeared, it provided the crew with an indication of what ocean current they were currently sailing through.

Fr Secchi was asked by the head of the Papal Navy to measure the transparency in the Mediterranean Sea. This task gave rise to the formalised measuring system.

Ever since the first measurement was taken aboard the Papal yacht in April 1865, marine biologists have used it to measure phytoplankton abundance.

So maybe all you need is a dinner plate, a tape measure, and your phone. Bon voyage!(Pro tip: don’t drop your phone in the ocean. You’re welcome.)