Category Archives: Jan2018

Urchin/Crab Panama Expedition 2018: Day 8

Laetitita taking a break

Today was interesting insofar as when I woke up, I didn’t have the faintest idea what the plan was.  This is a good time to mention that working down here requires…  flexibility.   “Let’s meet in an hour” could be hours later.  Between “Panamanian time”, miscommunications, translations issue, and bureaucracy let’s just say it can get complicated.   But… that all fades away when the boat heads out into the ocean.

Alexandra looking for crabs
Laetitia looking for crabs

So I joined Alexandra and Laetitia today to provide logistical support go fishing and take pictures.  Fishing was basically a bust, as were most of the underwater pictures.   But they had some great success with crabs today.  They found 4 different species, including a couple that represent geminate pairs with the Pacific.  So we’re up to 3 geminate pairs for the urchins as well as the crabs.  One particular hard-to-find species was hiding in a rock so Alexandra brought the entire rock back and then attacked it with a hammer at the station to extract the crab.  Another particularly challenging one resulted in Laetitia learning how to throw up in a snorkel mask while catching the crab.


After I did dilution-streaking of all the aerobic Caribbean urchin plates, Laetitia and I headed into town for an ATM and some souvenirs.  I bought a Panama hat even though I know they actually originate from Ecuador (they were very clear on this point when I visited Ecuador).

Had a visit at our dorm of a troop of about 20 howler monkeys which was pretty amazing to see and hear!

Hanging out near the kitchen

Another action packed evening of media prep, crab dissections, and some anaerobic culturing.  Tossed in a quick pasta dinner for myself and I think Laetitita had cereal for dinner.




Somebody is benefiting from the fire coral



Alexandra cracking open rocks
Looking for a cab in Bocas town in my new hat
Urchins and crabs together!
Aren’t these amazing looking?

Urchin/Crab Panama Expedition 2018: Day 7

Culturing from Eucidaris tribuloides in my awesome new shirt

A week in Panama today!  Sometimes it feels like a month.  Today we split up… Laetitia and Alexandra went to Boca del Drago to look for crabs.  They searched and searched without success but did find the missing Eucidaris tribuloides!  So now we have all the Caribbean urchin species that we’re looking for.  Meanwhile Jarrod, Jamie, and I went to scout out new sampling sites check out an organic coffee/chocolate plantation on Isla Bastimentos nearby.  Fascinating water taxi ride, it was us and a bunch of surfers and the boat took the surfers out (though some scary high waves!) to the break between islands where they would surf.  So they all paid the driver and jumped out, meanwhile a couple others paddled over and hopped in and went with us to Isla Bastimentos.   Cool.  The organic/funky/hippie plantation was amazing, we learned about the natural microbial fermentation of cacao which is pretty awesome.

A big one

When Laetitia and Alexandra got back, they jumped in the water near the Bocas Station and found a bunch of the crabs they need.

Mangroves: more interesting below the surface
Fish under the dock

After lunch was a lot of lab work.  I made new media, dissected/plated the Eucidaris, and made glycerol stocks/did DNA extraction on all the isolates from the Pacific.  Meanwhile Laetitia began dissections/plating on all the crabs they collected today.  Once I was done with lab work I jumped in the ocean to check out the amazing things growing in and around the docks.   This area is covered with mangroves and they are really awesome.  They’re not that exciting above water but underneath the are completely covered in the most amazing diversity of critters… including the crabs.

After dinner a group of us from the station took a water taxi to Isla Carenero to a restaurant called the “Cosmic Crab”.  Among other cool things, the lady that runs this restaurant is trying to create more demand for lionfish which is an invasive species spreading in many countries to the detriment of local fish.   There’s an international campaign (and push by NOAA) to create consumer demand for this fish, ever since I heard about the campaign I’d wanted to do my part for conservation and try the fish!  Anyway, I can verify that they are worth eating from both a conservation and culinary perspective.

Eucidaris, aka “the pencil urchin”
The dinner crowd
Laetitita photographing her crabs
Only 7 more minutes through the jungle to the cacao plantation
Schooling under the dock


Urchin/Crab Panama Expedition 2018: Day 6

Jarrod preparing to tie up to the mooring buoy
Turns out that Amazon sent Laetitita two left gloves
A sea urchin well hidden and protected from scientists
Corals and fish in the area

Busy day today.  Up early and a breakfast of borrowed PB&J since we hadn’t had time to shop yesterday.   Then out on the boat… the three of us along with a driver, Heather.  Pretty rough conditions… overcast skies and bouncing along big waves.  We made it out to Hospital Point on Isla Solarte and managed to tie onto a mooring buoy.  It was really not ideal conditions for collecting… big waves, low visibility and then it started to rain which made the visibility even worse and made it surprisingly cold.  I quit long before the other two because I was starting to shiver in the water.  It turned out to be relatively easy to find the two species of Echinometra (lucunter and viridis).  There were also a fair number of Diadema antillarum which are really a pain to collect since they are huge and sharp.  Jarrod got a nice one into our collection vessel (colander) with salad tongs.   But we couldn’t find any Eucidaris.  So we searched, and searched,  and searched.   We saw a lot of pretty fish, interesting corals (including fire coral… best to avoid that one!) but not Eucidaris.  We finally gave up and headed back.

Apparently the wind can make me look cool. Or something like that.
Free food!

Laetitita and I walked down the beach to a restaurant for lunch and hit the jackpot.  Turns out the restaurant had only very recently opened and so after we ordered our (cheap and delicious) food the owner came over and explained that she was teaching the kitchen staff how to make all the new dishes and would we like to sample them for free?  So she brought out little trays of all kinds of amazing and delicious things… like fish/yucca/cassava balls in passionfruit sauce and spiced plantain patties.   Then we loaded up at the grocery store and headed back to the station.

This was clean and empty before we arrived.

A lot of labwork this afternoon including dissecting/plating samples from the urchins, replating some samples from the Pacific, and preparing tubes for crab sampling.  I also tried (but failed) to set the lab on fire.   Alexandra Hiller arrived at the station today, so she and Laetitita will start looking for crabs tomorrow morning.

After the lab work was done, Alexandra and I headed downtown for dinner at a delicious Indian restaurant.  Jarrod was supposed to join us for dinner but got “stuck” in a bar for a few hours first.  We had some fascinating conversation about evolution, adaption, microbes, host phylogenies etc.  I think the the people next to us thought it was a bit odd.


Urchin/Crab Panama Expedition 2018: Day 5

Here’s what all the fuss was about

The suitcases arrived!  Just had to get that bit of information out of the way first.  So today started with housecleaning in Gamboa, prepping the plates for transport, and getting to the local airport (not the Panama City one).  While at the airport we got a call from Marcos Ramos who was the STRI contact working with the mysterious “broker”… who had obtained our luggage!  I have no idea if “taxes” were paid or what but Marcos was going to rush the luggage to our location.  Then a super helpful woman at Air Panama basically held our plane until the luggage came so we could check it to Bocas.  We were irrationally happy to see our stuff again.  And as a bonus, there were no problems getting it, or the stacks of cultured bacteria (buried under my dirty laundry) to Bocas.

Laetitia hard at work
Isla Colon

Landing in Bocas feels like “The Caribbean”. It’s a funky town with a chill vibe.  The buildings appear to be falling down and the roads are pretty bad but it just feels awesome.  We got settled in at the station and got our lab space and dorm rooms.  We got to work making up media and while it was in the autoclave we took a taxi down the road for a fabulous dinner at a beachside restaurant with Jarrod and his wife, Jamie.   Then back to the lab to pour plates and label tubes… tomorrow morning we’re off early on a boat trip for urchins and crabs.

A lab gecko on the wall
The dock at the Bocas STRI facility

Urchin/Crab Panama Expedition 2018: Day 4

Panama City from Naos Island

10:00am “Maybe tomorrow”

1:30pm “Probably by next Tuesday”

3:15pm “Good chance by Friday, but we need yet another official letter”

Those were the three main pieces of information we got today regarding the luggage, from three different people.  The last however is from the person talking directly to the “broker” who may send their daughter to the airport with the latest batch of paperwork.  So we’ll see.

From Echinometra coelomic fluid

Today was “let’s assume we never see our stuff again, what can we salvage scientifically?” day.  First of all we do have stuff happily growing on our “marine LB” concoction (20g LB powder, 15g agar, 10g NaCL, .5g KCl, and 2g CaCl if you’re wondering).  Anaerobic culturing is obviously out and DNA extractions are still a problem.

A gold mine! (Educational supply store)
The head shop where we bought sterilization equipment

So the three of us drove down to Panama City, to check out an educational supply store rumored to have Petri dishes.  They did!  As well as gloves, dissection tools, and a couple of other odds and ends.  Then Jarrod and Laetitita discovered that a head shop nearby had butane torches that would be awesome for sterilizing things.  MacGyver science!

Then on to the facility at Naos so that Jarrod could do some extractions, Laetitia could work on a review, and I could work hard on stuff go fishing.    A special bonus was that Alexandra Hiller was willing to drive our new acquisitions to Bocas so that we don’t have the same problem on the internal flight.  However, we will be carrying plates with the bacteria on them… guess we’ll see what happens!

Party time!

On the way back to Gamboa we got to experience the famous Panama City traffic jams… taking 2 hours to go 30 km.  Grabbed a quick dinner and then back to the lab for a late night culturing session to pick colonies in preparation for our move tomorrow.   We fly to Bocas del Toro so we can begin sampling from the Caribbean side of the Isthmus.


Urchin/Crab Panama Expedition 2018: Day 3

First of all… no equipment/luggage still.  Other than that, it was a relatively chill day.   We did some lab work in the morning (we appear to have some bacteria growing!) and caught up on e-mail.  After lunch, Laetitia and I went on a long walkabout.  First up over a ridge on a jungle trail… saw some monkeys and cool birds.  And tons of leafcutter ants… some awesome microbiology going on there! Then we ended up in the middle of a resort (which kicked us out).   Took another nature trail over to a big river which we followed the Panama Canal.  Pretty cool to see those giant ships go by!  Walked from there down the canal a couple of miles to a dock where I fished for a bit before being informed it was a protected area and being kicked out of there as well.

Finally cooked up the fish we caught in Taboguilla yesterday… amazing stuff!  If you ever have the chance to eat a finescale triggerfish that you catch, don’t pass it up.

Still trying to figure out how to do the rest of our work with no stuff.  We can wing some more culturing stuff but the DNA extractions would be tricky.  Wondering if the old “grain alcohol, meat tenderizer, and detergent” trick would be good enough for 16S analysis later?  Jarrod, Laetitia, and I had a 3 hour meeting tonight to discuss how to do the rest of the work assuming that we never see any of our stuff again.  I’m wondering if the UCD travel insurance covers things commandeered by a foreign government?

Urchin/Crab Panama Expedition 2018: Day 2

What a day.  Up at 5:00am, granola bars for breakfast and getting ready for the day.  Went down the visitors office only to find that our scientific visit hadn’t been approved and we couldn’t do any work.  Got that all sorted in a couple of hours and then raced off to the boat in Naos.  Headed out on an urchin/crab sampling trip with Harilaos Lessios, Alexandra Hiller, and a couple of divers.  Because customs had taken my snorkel mask I stayed on the boat… but that’s okay because I just fished for a couple of hours.  The sampling trip was a success… Haris collected several dozen urchins for his own work as well as representatives of the three Pacific species of interest for our project.  Those are Diadema mexicanum, Echinometra vanbrunti and Eucidaris tribuloides.  Alexandra and Laetitia were lucky enough to find a few porcelain crabs as well (Petrolisthes  agassizii).

Then the problems began.  Another STRI person went to the airport for our luggage and was rejected.  Now they want a “commercial invoice” from UC Davis and they won’t deal with any of us or STRI anymore, we have to work through a “customs broker” to “exonerate” our luggage.  What a mess.

We then went around the research facility in Naos and begged/borrowed some petri dishes and LB.  Then Laetitita stayed behind to dissect the crabs while Jarrod and I raced to the grocery store to stock up, then up to Gamboa.  He found an old tub of chemicals and we made a new invention “David’s marine LB” which we autoclaved (after weighing chemicals on ads torn out of a phone book).   Then off to our housing… which we couldn’t find!  We literally ended up going from dark house to dark house trying my key until we got in somewhere.  Grabbed some dinner and then headed back to the lab to pour plates, dissect the urchins, and plate out some (hopefully) bacteria.  Interesting process with no dissection tools, no alcohol, no flame (we eventually found a cigarette lighter).  Meanwhile Laetitita finished up in Naos and caught an Uber up to Gamboa.  We crashed after midnight… though were awoken in the middle of night by what Laetitita assumed was someone breaking into the house but was actually the living room light fixture falling and shattering.

Urchin/Crab Panama Expedition 2018: Day 1

An agouti outside our apartment in Ancon

So Laetitita and I arrived in Panama City ready to get settled in and prepared for our first day of sampling the following day.  However, it was not to be… we didn’t get out of the airport without problems.  As soon as the customs folks saw the petri dishes/tubes/extractions kits etc they freaked out.  Off we went into a little room filled with piles of contraband (the women ahead of us appeared to be arguing that there was a perfectly good reason for her suitcase to contain 13 empty new purses).  We argued and pleaded with several different people (almost all in Spanish… and ours isn’t very good).  Not only did they make us leave all the research gear, we weren’t allowed to use our cell phones to get assistance from the Smithsonian.   So away we went, checked into our STRI lodging, and went to get food.   From which we got picked up by Bill Wcislo, the deputy director of STRI, and back to the airport.  To get back to the contraband area we had to get employee access badges (in exchange for passports) and go through employee security.  However, they weren’t budging and his uniform and business card weren’t enough to relinquish our suitcases of microbiology stuff.