Tuesday, 29 January 2013

Go to graduate school

This could be the worst piece of advice you will get from this blog, because there is ample evidence these days that obtaining a graduate degree won’t get you a job (or not the kind you thought ). But I’m going to take the opposite tack, and tell you why attending grad school is not the worst idea you’ve ever had.

In 2003, I graduated with my BS in Environmental Systems/Earth Sciences from the University of California San Diego—a brand-new science major at a wonderful school. But I still felt totally stupid. Sure, I could derive equations. I had memorized all of the geological time periods. I knew what an anticline was, where to find siliceous ooze in the ocean, and that isotopes are powerful scientific tools. But did I feel like I could contribute intellectually to the world, as an environmental scientist? Not really.

While I did have some practical training in labs as an undergraduate, these were mostly (low) paid positions where I followed instructions, did repetitive, tedious operations (“now, attach together 10,000 of these tiny paired pieces of metal”), and didn’t have any involvement in looking at the results of the experiments. If this was the kind of work I could look forward to the rest of my career, I was not interested.

Of course, I had kind of always assumed I would get a PhD, for two reasons:

Have lots of containers, will travel for science.
1. I wanted people to take me seriously. As an environmentally-conscious and fiery kid (I am Italian and Irish, after all), I would get into heated debates with adults about why their choices were ruining the world for my generation. Of course no one listened to me, but I reasoned that once I was Dr. Carilli everyone would lend and ear (though the White House has yet to ring me for earth-fixing advice, for some reason).

2. My mom has a PhD, and she is awesome.

So, I applied and got into graduate school at Scripps Institution of Oceanography. After a year of pfaffing around and changing advisors and topics, I finally settled on a project that I was passionate about: applying my undergraduate background training in geochemistry, climate change, and oceanography to reconstruct the recent history of human impacts on the Mesoamerican Reef.

Within the first two years, I learned the majority of what I found to be the most useful parts of my graduate education. I probably should have just run away with a Master’s at that point, but I’m stubborn, and in the end I’m glad I stuck it out. While I may not end up in a job that actually utilizes my PhD (or any job at all—maybe I’ll end up a gentlewoman scientist and overly qualified mother), here are the parts of graduate school I am most grateful for, and why I think graduate education—even without a prized academic position at the end of it—is still worthwhile (major side note here—I am specifically talking about advanced science degrees, which include a stipend for living expenses and where enrollment fees are covered. In this economic climate, paying for a graduate degree is probably very risky):

1. I learned how to think critically.
I can still remember the gut-wrenching embarrassment during my first lab meeting with my tiny lab—myself, my advisor Richard Norris, and my co-graduate student Flavia Nunes. After discussing the findings of a paper we had all read, Dick asked me for my critique of the work. It had never occurred to me that I was supposed to be reading with a skeptical view of the claims the paper made; I had just taken it at face-value, like most of my undergraduate reading (The earth revolves around the sun: fact to memorize. End of story).

While there may have been classes I took as an undergrad that purported to teach critical thinking, for me it was ineffective. Maybe I wasn’t mature enough. Maybe no one had ever asked me what I thought about the strengths and weaknesses of a piece of scientific knowledge. It took many more months (years?) for me to get a handle on this, but our weekly lab meetings and small seminar classes were extremely useful to me for learning how to actually think.

Inadvertent grad school benefit: Devising more exciting ways to use luggage
2. I learned how to conceptualize, plan, and carry out actual science.
It’s one thing to say that I wanted to save the world by doing science. It’s completely another thing to know how to take the requisite baby steps forward to do that. What, exactly to focus on? Where I the world to collect samples? How many samples to collect? How to preserve them, how to prepare them for analysis, how to design the laboratory work? Then, how to interpret the data, especially when the answers aren’t readily apparent? How to place your tiny piece of work in context of the larger body of Science that other people have completed? How to build on your work to answer the next question that arises? None of these things can be learned in a typical classroom.
This is a scanning-electron-microscope picture of a piece of coral skeleton, from a failed project (of which I've had several). I liked being able to pursue projects that failed in grad school without fear of destroying my career.
3. I learned how to communicate about science.
At least, I like to think so. Giving talks and posters at conferences, lab meetings, and teaching, writing grant proposals and manuscripts for publication were all excellent ways to learn different styles of communication (aside from just arguing ineffectively with the guy in line at the bank about climate change, for example).

Over the entire six years of my PhD program, I also got to know some amazing people (those are links to just a few of them--I could go on forever there). I love watching their careers develop, and thinking of ways we can continue to collaborate together to create positive change for the oceans.

Grad school bonus: Instant nerdly friends/future unemployed people to have coffee with!
There are a lot of very bad reasons to go to graduate school, but also some good ones—becoming a potentially more effective scientist and/or citizen of the world, even though you almost certainly won’t continue on in academia because there are no jobs and no grant money. Despite an uncertain future, graduate school can, maybe possibly, be a good investment of your time.

My biggest regret is not listening more seriously to my advisor when he suggested alternative careers, coupled with not thinking seriously about what jobs (including those in academia) actually exist, or where my particular skills would best fit. Now, as the end of my postdoc looms, I am scrambling to find these alternatives, in case all of my various applications for academic positions are ineffective (which, given the odds, is likely). At least I always have those old cake-decorating and surf-instruction skills to fall back on.

Tuesday, 22 January 2013

Where not to dive

Because I research how human impacts influence the ocean, I’ve been to some pretty dismal dive sites. Human impacts include things like dumping raw sewage, trash, mine tailings, fertilizer and anything else we can think of into it; removing everything edible within reach of ever-more technologically advanced gear from it; and the global effects of changing ocean temperatures and acidification due to climate change.

Plenty of dive magazines and websites will direct you to the last remaining places in the ocean that still seem healthy and beautiful. But, if you’d like a realistic/horribly depressing idea of what our underwater world looks like when we don’t care for it, here are some of my favorites. You can also feel fairly certain you won’t see sharks at any of these places—those tend to be fished out quickly.

1. Near London, Kiritimati Atoll, central Pacific. 

Also known as the “Ulva Dance Party” site. Ulva, along with some other types of fleshy macroalgae (or seaweed), is used as an indicator for nutrient pollution. Here, “nutrient” refers to inorganic compounds like nitrate and phosphate—what you might use to fertilize your house plants. Where there are excess nutrients, whether from sewage or golf course runoff or perhaps changes in the way nutrients cycle through the food chain due to fishing, these kinds of algae flourish. Also helpful in the macroalgae-domination-transition is a relatively small herbivorous (plant-eating) fish population, due to fishing them out, too.
Ulva mustache

This site was also particularly nice when we were there, because of strong surge. In order to get down underneath the ulva and identify the few remaining live corals and the relict dead coral (we’re interested in whether these two groups are different), we had to either fight the current to stay in place for a moment, or try to go with the flow and identify on-the-fly as we rocketed back and forth across the transect. A combo of the two seemed to work best—watch the video to get a feel for what you are missing.

[I can't guarantee this won't make you seasick!]

Kiritimati does present some amazing coral-ogling opportunities away from the larger towns, however. So be sure to dive elsewhere to get an idea of how things perhaps used to look.
Coral bonanza!
2. Chachahuate, Cayos Cochinos Honduras.

Unfortunately this site is probably no longer as gross as it once was—the original “long drops” at the end of short piers on this tiny, rather densely populated sand island have now been replaced by composting toilets. So diving off of this caye may not get you an instant, roaring ear infection anymore, and the coral may be recovering. When I last dove here in 2006 – good lord, has it been that long?! – many corals were being smothered by sewage-fueled macroalgae and mats of cyanobacteria were marching over the substrate. But, there was also a cool wrecked airplane, and that kind of made swimming in poop-water Ok.
Part of the wrecked airplane, with hard and soft corals
The orange stuff is a thick mat of cyanobacteria

3. Western Teraina, central Pacific.

Kind of like the degraded part of Kiritimati, but replace the ulva with cyanobacteria and sea urchins. And intensify the surge. Note that urchins like to eat into dead coral; thus the effort of trying not to get stabbed while grabbing onto a section of dead reef to stabilize oneself long enough to attempt to identify said severely bio-eroded coral puts this experience in my top ten most exhausting endeavors. If you’d like to feel as though you’ve landed on a completely hostile aquatic planet, this is the dive location for you.
There are at least 8 urchins in this photo
Our surveys include identifying live and dead corals under a transect tape laid over (in this case, tied to) the reef

4. South Molle, Whitsunday Islands, Australia.

For one thing, you get to wear a neon “stinger suit” (see below) to prevent death by poisonous jellyfish. Also, there is very little to see because the water tends to be murky, so you may not notice that the bottom is mostly blanketed by, yet again, our friend macroalgae. My photos from our kayak-camping-snorkel adventure (seriously recommended, what fun!) have been lost, so you’ll just have to imagine this one. While the outer Great Barrier Reef far from land is still quite spectacular in many of the less-trampled locations, sites close to land tend to be less coral-reefy and more algae-field-like.
So stylish! I stole this photo from somewhere online and then forgot where. Sorry, dudes

5. Bikenibeu, South Tarawa, central Pacific.

If you ask at the hospital, you can probably be directed to get as close to the main sewage outlet as possible. The best thing to do is free-dive at this site, preferably without fully clearing your ears so that you perforate an ear drum—all the better to get a most impressive ear infection that requires five types of antibiotics to conquer. Aside from the thrill of bobbing at the surface, being tossed around by large, fierce ocean swells offshore of an island in the middle of the Pacific, you can also see an interesting example of coral monoculture. Though there is fairly high coral cover (and not as much macroalgae as some of these other sites), it is mostly all one species—kind of like an underwater cornfield. Since coral reefs are usually considered the “rainforests of the sea,” with extraordinary diversity, you are correct in thinking that an underwater cornfield probably doesn’t function the same way as a more intact reef. 
Lots of Porites rus - and not much else.

Sadly, this is only a short sampling of places humans have very obviously degraded the coastal ocean. These effects are not restricted to coral reefs, either (it just so happens I know most about them). With conscious effort, the trajectory towards degradation can perhaps be reversed…but first it has to be recognized. Wherever you next stick your head under the water, give a good think about whether what you are looking at is healthy. Do you think it looks the way it has always looked? Or can you see dead ghosts – a lack of fish, large dead empty shells, old corals covered in algae? It’s hard to know what was there before, but that’s where my kind of work comes in—to use a form of environmental forensics to figure out how things have changed, and why. 

Tuesday, 8 January 2013

Why geochemistry is awesome

Yesterday, I had a new paper come out online in the journal Coral Reefs. I’m really excited about this paper because (1) it’s been a very, very long time in the works and (2) I think it’s pretty neat. I also think the manuscript is pretty dense, so I’m going to make a stab at explaining it simply so that you, too, think my work is neat.

Geochemistry is a science in which we collect samples of natural things – rocks, shells, feathers, bits of wood, teeth – and then measure some aspect of their chemical makeup to learn something about the world. Geochemistry can be used to learn about the organisms whose parts are being analyzed; for instance to figure out what they ate (the old adage “you are what you eat” is true here—many times a distinct chemical signature comes with eating certain food items). It can also be used to learn something about the environment in which an organism lived or a rock formed.

Requisite beautiful-coral-reef shot. Kiritimati Island
Corals are, by geochemistry-practitioner standards, awesome. For one thing, corals make their skeletons out of chemicals in seawater—as the water chemistry changes, so does the chemistry of the skeleton. Second, corals grow larger over time by adding new layers onto their skeletons, while the old skeleton often just sits there as a semi-permanent record of conditions at the time that bit of skeleton formed. This is like keeping track of daily weather on slips of paper added to a pile—you can then dig back through the pile to see how things have changed over time.

Third, corals also have a built-in time-stamp on these records: the density of the skeleton fluctuates with the seasons, leaving bands that can be seen by x-ray or CT scan in samples (see my earlier post). For coral samples collected live, these bands can be counted back in time; corals that are dead can be dated using another aspect of geochemistry: the amount of a particular radioactive element that decays at a known rate can be measured to back-calculate how long ago that coral was alive.

The fourth excellent/horrible thing about corals is this: while they sometimes act as passive recorders of water chemistry, both the density and the chemistry of the skeleton can also be affected by other things – notably how happy the coral is (corals that are heat-stressed “bleach” by expelling their colorful symbiotic algae, which screws with skeletal growth and chemical incorporation). Other aspects of coral biology such as spawning or food intake also can change the chemical signature.

If all of the different influences on the coral skeletal chemistry can be disentangled, there is fantastic potential for long reconstructions of both the environmental conditions in which the coral grew and the coral’s reactions to those conditions (over the last few100s of years, or even longer if dead corals are also used).

But that’s the hard part: disentangling. For one reason, we keep thinking that we know what controls each chemical signature (and this is the “royal we,” including me and other scientists), and then we figure out that it’s more complicated: we thought the concentration of strontium was a direct, unbiased measure of water temperature; now it seems that this is also very slightly affected by the skeletal growth rate. We also thought that the ratio of two different isotopes of oxygen in the skeleton was only controlled by water temperature and salinity (isotopes are different forms of the same element that behave the same chemically but have very slightly different weights), but then we figured out that calcification rate also matters.

Not totally happy coral
And here’s where our work comes in: faced with weird oxygen isotope data that couldn’t physically be explained by any combination of water temperature, salinity, or calcification, we knew there must another as-yet-unidentified impact at play. What we saw was a big jump in the baseline of the data after a major coral bleaching event.

Now, a quick tangent: coral bleaching is an extremely worrying phenomenon. Corals get most of their nutrition from the symbiotic algae they house in their tissues; when bleached, they can starve to death or become more susceptible to disease. With global water temperatures increasing, coral bleaching is becoming more frequent. The big question in the survival of coral reefs as we know them is therefore: can corals adapt?

One way corals might be able to adapt to warmer waters is by kicking out “weak” forms of symbiotic algae and trading them for genetic strains that are more resistant to heat stress. This is called the “adaptivebleaching hypothesis”—the idea being that by acquiring more heat-tolerant symbionts, corals can survive the onslaught of climate change (at least for a while).

 Our data might be a reflection of this very phenomenon. If the symbionts the corals housed before the bleaching event were physiologically different than those after, maybe the skeletal chemistry would be different.

There has been a lot of activity lately from scientists trying to understand the nitty-gritty workings of coral calcification. We were able to synthesize this work and put forward a potential mechanism that could cause our observations (based mostly on a change in pH at the calcification site).

We also tried to test the idea directly by collecting lots of little nubbins (possibly the best technical term ever) of live coral. We identified their symbionts using DNA methods (and here “we” means my colleague Melissa Garren), and then the corresponding oxygen isotope values. What we found was a hint of a relationship—so we didn’t disprove our hypothesis.
Our "nubbins" were essentially mini-core samples from large corals

This area of research still needs more work, but it is exciting; if this signature is real, it could be used to retrospectively test for adaptive bleaching in other corals during other bleaching events. This is important to predict the outcome of bleaching events and manage coral reefs as we face increased heat stress. If corals can adaptively change symbionts, can we help them do this? Can we more effectively manage outplanting and reseeding efforts to restock damaged reefs?

I hope that this paper stimulates new ideas and more projects to help answer these questions.

Sunday, 6 January 2013

Cheer the hell up

It’s a New Year! Yay! Everything will be better! Or will it? Not without your efforts, I dare say. Inspired by reading “The Happiness Project," I thought I’d share a few ways I force myself to feel better when I’m in a crappy mood. Because no one likes a grumpster.

1. Keep a box—either in reality or in your head—in which you store ridiculous items that are guaranteed to make you laugh. Some things that I like to draw upon include a (new) tampon that went through the dryer and achieved the size of a teacup poodle; the incorrect way my friend Vanessa used to pronounce “sachet”; the brilliant cartoon book Unpleasant Ways to Die (side note: this book is also used as a test for whether people I know have a sense of humor).

2. Go outside with the express purpose to find a beautiful natural object. Almost everything natural is fascinating up close, so take a magnifying glass if you have one. I find that after focusing on the iridescence of flower petals, the patterning in clouds, and the range of colors in fall leaves, I sometimes forget why I was in a foul mood in the first place.

If things like this exist, the world can't be all that bad.
3. Make a fake phone call and tell the pretend person all of your problems. They will probably sound ridiculous out loud and you can laugh at yourself and move on.

4. Eat a very ripe piece of fruit with abandon, getting juice all over. Maybe this dredges up the carefree feeling of being a kid, or just helps grown-up problems seem dumb in light of all that juicy goodness…but this always makes me happy.

5. Never underestimate the power of coffee, chocolate, and/or wine, preferably in company of a friend, a good book, or a stupid movie.

6. Look at cute pictures, videos, or go visit some baby humans and animals. Not only is it hard to frown after snuggling a kitten, it might actually increase your productivity afterwards, boosting the satisfaction of your day another way! 

7. Do something a little scary. Learn to surf, go to the Bug Zoo, get a radical haircut. Succeeding at something scary is a great way to boost your self-satisfaction, and the adrenalin will also give you a short-lived buzz to kick you out of your fog.

I did say a little scary. This is too much for me, but may be just what you need.
What is your anti-funk strategy?