Woodfall project summary and status update

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Hi all! The semester is nearly over and man oh man has it been a busy one!

The main project occupying my time has been the woodfall project. For a recap and update of how it’s going, check out my post on the University of California Museum of Paleontology website. Then check out all the other cool stuff  graduate students, museum scientists, and faculty in the museum are doing!

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Woodfall after 2 years at 3200m, about to be collected. Credit: Still taken from MBARI footage by Jessie Kendall-Bar

Marine lab mania

Banyuls-sur-Mer at sunrise, the marine lab is the big white building on the right.
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Flashback to June 2012 —

I have just finished my wonderful week as a snail apprentice in Stockholm and I am feeling greatly inspired and ready for my next adventure, which is rapidly approaching. I am off to a marine station in the south of France for 10 days with my German mentor and colleague, Gerhard Haszprunar. When I booked my flight from Stockholm to Munich for June 17th with the knowledge that the trip to France started on the 18th, I thought, “oh, an afternoon and one night’s rest will be plenty before the drive down.” But wait — the 18th is actually when the course Dr. Haszprunar is teaching STARTS…IN FRANCE…so in actuality I had approximately 4 hours between landing in Munich, and getting to the museum to hop in a van for the 15 hour drive down to Banyuls-sur-Mer, France, right on the border of France and Spain, Mediterranean side.  Anyway, it all worked out, but it goes to show how important getting your details straight before booking flights really is and maybe I should give myself more of a buffer for future trips.

Ok, so although the drive was exhausting (even though I just had to take shifts being an attentive co-pilot since I couldn’t drive the van), we arrived in Banyuls about an hour before sunrise and man oh man was it worth it to see that! Continue reading

why you should sweat the small stuff

Stockholm at sunset, which lasts forever in the summer.
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Anders and I at the banquet of the World Congress of Malacology this summer, wonderful conference, more on that later!

Well for one, when it comes to benthic marine samples, animals smaller than 2.5 mm make up most of the catch according to Anders Warén, and coming from a man who’s been on countless research cruises and participated in over a thousand dredge hauls, I’m inclined to take what he says quite seriously.  The sad thing is that most researchers throw out this precious (and almost always partially unknown) diversity with their salty bathwater after picking out the specimens you can see with the naked eye. As someone who chose to work on a small sized group of animals for my dissertation because of

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the infamous binders – these are filled with photos of snails and radulae and other information and I believe have traveled the world with Anders as valuable references on research cruises (now luckily he has a laptop).

the fascinating way in which they have adapted to live their lives, I already appreciated them to some degree. But even after only a few days of sorting through samples in the company of one of the world’s experts on small molluscs, my appreciation has grown immensely for the care, attention to detail, and love of the natural world’s tiny curiosities that is required to learn all that we can from these little beasts. Continue reading

That awkward moment…

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…when you get an email from wordpress telling you to moderate a comment (a spam comment, but still) and reminding you of the existence of your blog. I then logged in for the first time in probably a year and out of curiosity looked at my stats and was completely shocked to see that people have actually looked at this thing, then shock turned to embarrassment…I realized I have a backlog of post ideas in my head and it’s time to finally end this hiatus and get ‘em out there. Thus, by writing this first post I am telling you (but mostly myself) that I am going to look back and post the things I should have posted months ago. Bear with me if the posts to come are old news (it’s definitely old news), but I need to catch up before I can keep moving forward, right? Or am I screwed already since you never get anywhere even if you run as fast as you can and I already stopped running? We’ll go with the first scenario just because I like to pretend to be an optimist.

Anyway, I’m back!

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“Snails? well, that sounds boring…”

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“no stress” chocolate snail in a shop in Zurich, clearly a city that knows snails are super chill

During my travels this spring and summer I’ve met a lot of people, and inevitably they want to know what I do. Usually I start off pretty vague, not knowing if they really care that much about the details of my research and if they ask enough followup questions I eventually get to “I study the evolutionary history of a group of small deep-sea snails that live on strange substrates like wood, bones, worm tubes, etc etc” and some people respond with something like “wow! that sounds really interesting!” and I am glad they think so since their tax dollars are paying for it, but others say something like “snails? that sounds boring*”  or ask in what way they are helping humans like “can you eat them?” or “oh, are you hoping to use them

cool enough to be Berlin street art ;)

for medicine?” which tends to make me feel like I have to defend my research and explain why studying the natural world is important generally, not just for direct benefit of the human species.

For one, as the number one threat to Earth’s diversity, I think humans have a certain responsibility to understand it and how it evolved, this may even

help us preserve what’s left of it, which in the end actually helps the human species, so people who study diversity are really doing the rest of y’all a favor ;)

For two, snails aren’t “just snails” they are a tool I am using to understand evolution in poorly understood environments, which yes, are NOT directly relevant to humans, but are a piece of the puzzle when it comes to understanding how we get diversity in habitats that are difficult for most animals to live in.  By the way, if I were studying the exact same question in some brightly

I will make you appreciate the natural world! I will! (street art in Berlin)

colored vertebrate group, like birds of paradise, African cichlid fishes, or even lizards, I doubt I would get the “that sounds boring” response.

I could go on about the reasons to study the world we live in, but I have a feeling most of you (people who are reading this) are already supporters of basic research and have your own reasons why you think it is important, or maybe you have arguments for why it is less valuable than cancer research. Either way, I would love to hear from you in the comments. This is a topic that often has quite variable views depending on your perspective and experience, and I find that fascinating.

By the way, if you have the impression I don’t enjoy meeting those people that don’t appreciate basic research, I actually really do! I try to see every encounter in a beer garden, on the chair lift, at a party, or basically any situation where someone ends up actually asking about my research (I don’t just go around talking about how cool snails are, I don’t think I would have any friends or convince anyone that they are…I would just be crazy snail girl…maybe I am….meh…I digress), to show them that snails aren’t as dull as they seem, and not all marine biologists study dolphins, and you don’t have to be curing cancer for your research to be important ;)

*one of these interactions was at a beer garden in Munich (I love the atmosphere at beer gardens, so relaxed) and this response was from a couple of engineers who couldn’t tell me what was so interesting about what they did (I do appreciate that engineering is important though, nothing against engineers, to each their own) and then proceeded to ask me more questions about my boring snails, guess they aren’t so boring once you get to know them! This is the lesson though, you’ve got to give the little things a chance before you will see that they are amazing! Or simply appreciate that there are many interesting things in this world and different people that find them interesting, it would be pretty boring if we all had the same interests and did the same things no matter what it was.

Painting my way to a 3D limpet

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I’ve been in Munich for the last 3 months, three months to turn histological limpet sections into a 3D anatomical masterpiece (and enjoy living in charming Bavaria).  I’ve been so busy enjoying my work, the people, and my general surroundings that this is the first chance I’ve had to try to summarize what it is I came to Munich to accomplish.

View of Munich from the top of Alte Peter Tower

Alright, so last summer I was in Japan reconstructing a limpet in 2D with the oh so modern tool, a box of crayons. This spring I graduated to using a program (AMIRA) that is quite reminiscent of the computer program “Paint” to make a 3D anatomical model of one of the tiny snails I study.

Basically this is how it works:

1. Put your specimen in a block of plastic

2. Slice that block of plastic very thinly and put the slices on a glass slide

3. Stain those slices so you can see the bits inside (these were ready for me beforehand, by about 10 years)

4. Take photos of every other slice or so keeping the magnification constant

5. Align those photos to make a stack, kind of like an MRI

Two overlapping slices in contrasting colors so you can check to make sure they are all lined up right

6. Now you can scroll through the image stack and identify organs and follow them through the specimen

7. Paint over each organ using different colors, you can skip a bunch of slices and the computer fills in the gaps for you to make nice smooth links

each organ is labelled with a different color following it all the way through the animal

8. Once all the organs are labelled through all the slices, you can isolate each one and make it look smooth and pretty and then put them back together again to show all the parts together or as separate organ systems.

looking at the reproductive system from the right side of the animal

9. Voila! Now you have a 3D model of your tiny animal that once had very difficult anatomy to visualize and the use of so many cool tools to measure volume, surface area, shape, and generally just have a better understanding of it’s morphology and ways to actually quantify that morphology.

ta da!

Although this was quite a time-consuming process, tools like AMIRA and other 3D reconstruction software allow us to quantify and compare morphology more precisely . More and more, evolutionary biologists are relying on molecular tools (which are great too!), frequently alone, to infer evolutionary patterns. However, it is morphology that will tell me how a snail’s digestive tract has changed and whether that might have something to do with the substrate it’s living on, whether it’s teeth are acting like saws or are so reduced that they are essentially non-functional, or any number of other morphological characters that are directly relevant to how the animal interacts with it’s environment and other organisms in it’s vicinity be they predators, competitors, symbionts, or parasites. Of course, molecular tools are needed to further elucidate many of these relationships, but how will you know there is something to elucidate unless you are first able to observe it? Some things you would never even recognize without actually “seeing” them!

Making science out of chucking stuff into the sea

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setting off on the Western Flyer for an epic adventure!

What kind of stuff you might ask? Plants! Basically, many deep-sea beasts have specialized to live on woody substrates and I wanted to test whether the kind of plant matters to the beasts that colonize it by sinking several different plant species in deep water. Please see my previous post on why land plants are important to deep-sea critters for an explanation of why I wanted to put woody stuff in the ocean and how I prepped it for sea. One thing I forgot to mention is how I actually tracked down the wood I wanted to sink. I basically emailed or called every tree service in Berkeley and got in touch with the local botanical gardens and the city.  The most difficult thing to find though was tree fern and I was lucky that there is a tree fern enthusiast right here in the east bay who has a website called Ferntastic! and happened to have a chunk of dead tree fern I could sink. Amazing wood resources aside, I was able to get material from ten different plant species, get them prepped for sea and down to the Monterey Bay Aquarium Research Institute where I would be setting sail with Jim Barry et al and Craig McClain (Dr. M) on the Western Flyer.

Gumby suit! standard newbie procedure…

There were several objectives for our 6 day voyage including doing transects and collecting animals from varying depths for projects in the Barry Lab, resetting the FOCE experiment, retrieving logs that had been sunk by Dr. M 5 years previously, and sinking the plant material I had collected. In Dr. M’s excellent post on Deep-Sea News, you can read all about the whole process of wood community formation, from how the wood gets to the bottom of the ocean in the first place to the community that colonizes it and the holey remains those critters leave behind.

I’ll give you a sense of what the cruise was like and the ups and downs that are inevitable when doing deep-sea research:

Wood deployment was slotted for the second day, so while others were retrieving experiments and setting up sea urchin races (FOCE is like a racetrack with lanes and hurdles  for sea urchins with tasty kelp at the other end and different concentrations of CO2), Dr. M, David Honig (a graduate student at Duke working with Dr. M on the wood we would pull up), and I tied polypropylene rope to the wood bundles to help the ROV pilots grab the bundles with the ROV arm and loaded it up into the elevator.  One lesson I learned is that you can never bring enough zip ties on a cruise, we used them to secure knots in the rope, attach rope to the mesh to prevent slipping and then secure the bundles to the sides of the elevator, which you’ll see was a key foresight by Dr. M given the next morning’s events.

Prepping the bundles for deployment, thanks guys!

zip tying bundles to prevent jostling (and escape!)

6am the next morning: The crew is on the back of the ship getting the elevator set to sink and the ROV Doc Ricketts is being deployed to go find the elevator on the bottom. I watch as the crane lifts the elevator with all my wood bundles off the back of the ship and down into the water. Now, the surface is the roughest part of the journey, and the latch holding the bundles in came loose! Good thing we zip tied all those bundles to the sides of the box! Only bundle number 20 escaped, and I thought we would lose it, but miraculously it got caught on one of the elevator’s screws and came back up safely onto the deck.  After re-securing the latch, the crew was able to deploy the elevator with no further incident, and it would be 2 hours before the ROV completed its 3200m journey to the bottom, so breakfast time! One thing about research cruises is that there is no chance you will go hungry, Patrick, the ship’s steward, prepared three delicious meals a day and then there were plenty of things (including a dedicated ice cream freezer) for your snacking pleasure.

2 hours later I step into the ROV control room, think mission control, three pilot chairs face a wall of monitors tracking the topology with radar, the position of the ship and ROV, changes in water temperature and chemistry, and several different camera views. Two of these chairs are occupied by ROV pilots who fly the ROV and use all the manipulative features like arms and suction hoses to do the bidding of the scientists (muah hahaha). The third chair is for someone to control the HD camera and make sure it’s focused where the ROV pilots need it (I got to sit in this chair a bunch, which was really exciting!). Behind those chairs are four airline chairs for spectators and people taking notes or directing what they’d like the ROV pilots to do.

The ROV control room, feels like you’re down there with the ROV!

The ROV is at the bottom tracking the elevator with a beacon and the radar (the elevator isn’t that big, but it’s so flat down there it shows up pretty strong on radar). The pilots have found the elevator and all the bundles are still nestled safely inside, phew!  Now to get those babies out on the sea floor to start being colonized. Basically, the pilots used one of the mechanical arms to unlatch the lid and then put about 10 bundles in the drawer of the ROV, then they dropped them in a line about 3m apart from eachother as if it was a paper route, just dropping them a little above the seafloor and letting them lie. We nabbed a picture of each one and then went back and did this two more times to get the rest out.

Okay, so every time I’ve told someone about this project the first question I get is, “how are you going to anchor the logs?” or something similar, but here’s the thing, the pressure increases by 1 atmosphere (ambient pressure is 1 atmosphere) for every meter of water, so by around 100m deep all the gas in the logs that would cause them to float is pushed out and replaced by water, at 3200m this is no problem. Also, the currents are so slow that we are not too worried about the bundles being swept away. So with the new bundles successfully deployed, we could use the rest of the dive to retrieve Dr. M’s logs that he had sunk 5 years ago and see what goodies they contain. Based on the cliffhanger at the end of his post I think we all have something exciting to look forward to!

Dr. M breaking open the wood to find the goodies inside

Before I sign off, I have to tell you about one other unexpected hiccup that happened at sea. You remember the problems we had with the latch on the basket of the benthic elevator? Well, it was still a problem when it came back to the surface with Dr. M’s logs in it and by the time the ship made it over to the elevator, three logs had been lost and sunk back to the bottom. We thought we would never see them again…but after doing some work at another site the next day we took a reaaalllly long transect back towards the “Deadwood” site, and guess what?, the ROV pilots found all three logs! Isn’t that amazing? Thinking back to last October, I’m still amazed they found them, and Dr. M was so happy after being so upset over the loss of data.  So all in all, a great first research cruise for me and I hope to be getting back out there in  a year and a half or so to retrieve the wood that is sitting on the bottom…hopefully attracting many interesting beasts.