Monday, August 29, 2016

And then there was the lab ..

So of course; urban exploring in Jerusalem, desert hiking in Jordan, afternoon strolling in Acco, scuba diving whenever; it's all great and fun. Sounds like we're just on 2 months vacation right ?
But, oh dear, no. There is also plenty of work to be done.

My coral experiment came to an end with a total of 95 coral fragments sampled. A fair amount for a full month of experiment. But also a fair amount considering the time it will take to prepare all the samples for analysis.
So now it's time for some lab work.


So I went to Ben Gurion University of the Negev Sede Boqer where there is a large department for research on water resources and where my collaborator Edo Bar-Zeev is working. 
That ended up being 4 days of intense lab work.

A lot of people probably don't realize of much work there can be for doing one specific analysis (and why would you know if you've never done it?!).
For example, I am analyzing the protein content in my corals. The analysis it self is easy enough: You make a standard curve of know protein concentrations you get from a kit, add some specific solvent that reacts with proteins and a machine reads the output.



The preparation though.. First your sample needs to be diluted into pre-made solution. Unless your sample is still in liquid, then you'll need to centrifuge it for at least 20 min so the cell material sinks to the bottom and you can discard the liquid.
Then you need to break the small cells so the kinetic analysis solvent can react with the proteins inside the cells. To do this you need to sonicate the sample (burst it with ultrasound waves. Sounds like the dentist from hell) for 1.5 min, but in intervals of 30 sec so you don't heat up the sample. Then you need to centrifuge again.

Now you are ready to prepare the plate of samples that goes into the analytic machine. That means pipetting 10 µL of the sample into a tiny well on a plate. That's the size of a small drop. Then add the kinetic solvent but as fast as possible to all of the samples so they will have the same reaction time.

So time this up with 95 samples and you have a full days work! The sonication alone is almost 3 hours and with the pipetting and centrifuging its well after lunch time when you're ready to read your samples on the machine.
The read it self is only 2 min which makes the 5 hours of preparation seem even more intense.

 Sonicating 95 samples
And then of course I have two different protein samples so it was more like 190 samples.

The last lab marathon happened last week. Trying to get a big bunch of samples prepped and analyzed before heading back to Santa Cruz. It ended with two intense lab days: First day to finish the last of the protein analyses (this time only 12 samples - phew!) and calibrate the instrument for our bacteria and plankton analysis. The second day I started at 7:30am labeling vials. We thawed half of the samples we had and started prepping them. At 4pm we could run the first analysis. At 7pm we started the second. At midnight, the third and last. At 4am I shut down the machine and went to bed.
A nice 20 hour work day. I won't even try to explain how hard a day like that is. It won't do it justice. Once samples are thawed there is no turning back. So take home message: Don't thaw too many samples at a time!
The bright side is: We have data! Now "all" there is left is to look through the data and make sense of it.
And I will probably return to Sde Boker sometime in Winter to finish the last half of my samples in the freezer..















Tuesday, August 23, 2016

The Streets of Tel Aviv

Weekend before last, I took a trip up to Tel Aviv for fun. You might expect a post full of pictures of the beach:
The view north from Jaffa
Or perhaps these of the Carmel Market:




Shakshuka + beer = happy Dan
So there are those pictures. But more unexpected to me was all of the interesting street art I saw in the city, particularly in the morning when I walked from the neighborhood near my hostel to Yafo (Jaffa). As a native of the Los Angeles area, I became an admirer of the medium of street art at an early age. Tel Aviv is full of the typical tags and stencils, but also whimsical, abstract creatures which jump out to confront you at every corner. As is typical with street art, there are probably many inside jokes here that I am not party to. While sharing an irreverent, anything-goes mentality with LA street art, the examples I saw in Tel Aviv seemed more playful rather than sardonic. Here are a few of the particularly cool examples of art that I saw.














Friday, August 19, 2016

Roundabout Roundup

Satellite view of Eilat. I've marked all the roundabouts in red (not counting cul-de-sacs)
Eilat may be famous for its beaches, reefs and heat, but if you spend any significant length of time here, you'll quickly realize that the true passion of this town is its roundabouts. I have been to a good number of cities in the world and have never encountered the density of roundabouts that I see here. The 4-way intersection is a rarity here; almost every intersection is dominated by a large circular traffic island, many of which are whimsically decorated by different local institutions and groups. Here are a few roundabouts we've seen as we've driven through town. I'll post more as I see them!
Roundabout sponnsored by the local Freemasons chapter

In front of Dolphin Reef


Sponsored by the Underwater Observatory

The Women's Roundabout

One of many roundabouts with native animal statues

An elaborate roundabout with waves, jumping dolphins and an elaborate sculpture at the center

Thursday, August 18, 2016

Clamples!

A thick, hearty slice of Tridacna maxima
During my time in Eilat and Aqaba, I have obtained many shell specimens. For my work, I only need a section of shell exposing the growth bands along the longest axis of growth within the shell. Whole shells would be impractical to take back to the US, and my permits here only allow me to take pieces of shell. Back at UCSC, we have a large radial sawblade specifically for cutting geological specimens to make thin sections. Unfortunately I do not have access to such a blade here, so we've had to think creatively!

Photos by Michele Markowitz.
The scientific technician here, Moty Ohevia, devised a setup for me using a 4-inch blade on a pneumatic cutter. Being powered by compressed air is safer than electricity because I can use water to cool off the blade and sample. The blade is dull and turns slowly, which means I'm not at risk of losing my finger for science. But it also makes a big mess and is noisy, so I am using eye protection, a mask to keep out dust, earplugs, and close-toed shoes for safety. Other members of our group including Noam, Adina and Michele (who took these pictures) have been helping me by holding the power trigger on the drill and spraying the sample with water as I direct the sample over the blade.

The slow spinning action also makes for a very smooth cut. When I return to UCSC, I will be sanding down the surface with sandpaper and fine grit on a rotating wheel, to make the surface smooth enough to see very fine growth increments. I believe some of these increments are formed over fortnightly (14-day) tidal periods! 
Acetate peel of a Tridacna maxima shell. To take a peel, the shell surface is sanded very finely, etched with a weak acid, splashed with acetone and stuck to a sheet of acetate. After applying pressure while drying, the shell is peeled off and a thin layer is stuck to the transparency, making fine growth bands more visible. I took this picture through a hand lens to show the fine growth bands that can be seen in the shell.
Counting these bands will allow me to measure the clam's rate of growth. I will then use a computer controlled micromill to sample from these bands. The micromill is basically a little robot that drills exactly where I tell it to with a dental drill bit, at sub-millimeter resolution. I will collect the powder from the drilling and use a mass spectrometer to create a very detailed record of carbon and oxygen isotopes. These isotopic records can be used to reconstruct the clam's environment and physiology during its life, including whether it had to regularly had to stop growth due to temperature and other sources of stress. 

Tuesday, August 16, 2016

The Aqaba Adventure


Aqaba is Jordan's only coastal city. Until recent decades, it was a sleepy coastal town, but the rapid development of industry and tourism in Jordan has necessitated a large port city, and its reefs and proximity to important archaeological sites like Petra make it a sought-after destination for tourists. As a result, Aqaba has become one of the fastest-growing cities in the region.

Aqaba hosts the world's sixth-tallest flagpole (according to Wikipedia). It is indeed huge and easily visible across the Gulf.
Aqaba is also an important center for marine research. The studies on the giant clams which inspired my initial idea to come to the Red Sea were largely conducted on the short 16-mile strip of Jordanian coastline. Along this coast, impressively large modern reefs host the three species of Tridacna described from the Red Sea.



Two lionfish
During my time in Jordan, I stayed at the Marine Science Station (MSS) just south of Aqaba. MSS is a government-administered institution hosting marine researchers from the University of Jordan and Yarmouk University, and also hosts a marine reserve and aquarium.

Black-tip reef shark

Directly inland from the coast, fossil reef terraces representing ancient reefs are have been exposed by tectonic uplift. These terraces resemble steps descending into the ocean. The oldest are over 120,000 years old, predating Homo sapiens' expansion into the region. Comparison of the fossil and modern bivalves will allow us to determine their change in growth rate through time.
View from the top of one terrace. The coastal road lies atop another terrace, around 6-10 feet below, and the modern reef is submerged below that. Someday it will be a terrace as well.

My work in Jordan consisted of two parts: collecting modern and ancient shells of giant clams for growth band counting and isotopic testing back in the states, and diving to nonlethally sample hemolymph (body fluid) from living clams. The modern diving went off without a hitch. The clams were largely unaffected by the sampling, reopening their shells to expose their mantles and filter-feed shortly after being sampled.

Collecting modern shells was also easy. The beach is covered in valves of recently dead Tridacna of various sizes. I gathered specimens of all three species and cut small slices of shells to take back with me to America. I even found some likely fossil specimens embedded in rock directly on the beach!

Where it got more complicated was when I sampled fossils from one of the uplifted reef terraces. I was dropped off and went to work chipping fossils out of the reef. About 45 minutes later, two police officers drove up and asked what I was doing. Unfortunately, we suffered from a complete language barrier. It would be hard enough to explain the purpose of my research in English, and so despite their best efforts to communicate via Google Translate on our phones, they took me to the Aqaba police station.

I waited in the break room and they called in my collaborator, MSS Director Tariq Al-Najjar, who came in and explained in Arabic what was going on. Apparently, someone had called in worried I was prospecting for gold! Even in the States, this is an issue for fossil hunters. Everyone in the police station including the chief learned a bit about the fossil reefs and Tridacna that day.

We waited for an English-speaking member of the city's dedicated tourism police to arrive (it was Saturday morning and his day off). He had a master's degree in archaeology and was very familiar with the principles of scientific excavation. After taking my statement in English, we were free to leave.

Throughout the experience, I was pleasantly surprised at the politeness and professionalism of the Aqaba police, in contrast to my limited but negative experience with the demeanor of police in the United States. They were extremely professional and dedicated themselves to figuring out how to confirm that this strange bearded American visitor in shorts and a broad-brimmed hat was not there to steal Jordan's minerals, but actually there to research their coastal environment and collaborate with Jordanian researchers. When they asked me if I had any complaints, I assured them that I had nothing but praise for their professional conduct!

Though the morning was gone and the heat was now becoming oppressive, my collaborator Tariq took me back to resume where I left off, and I found a few more specimens along the fossil reef terrace. My fieldwork turned out to be a great success, despite my extremely unusual morning.

I am very grateful for the hospitality of everyone I met in Jordan, and am still in awe of the incredible natural and cultural beauty of the country. I will definitely be back, and maybe take a course in Arabic in the meantime!
Our group with Tariq!

Friday, August 12, 2016

A City Lost In Time


Jerusalem has been on my top 10 of cities to visit for a long time. Not to go pray at some holy relic. I’m not religious, have never been and doubt I ever will be. Not to visit museums. I’ve never really had the patients for that. Not to go shopping. There are so many other places to do that. 


I wanted to visit Jerusalem to be in the center of history. To feel and experience the area that claims to be the birthplace of religions that ultimately shaped the modern society. To see the ancient ruins and marvel at churches and mosques built with a finesse and technic that makes me wonder if they perhaps used magic to make it all stand straight. To try to grasp, maybe just a hint, of why people still strive to this place with their beliefs and why people are still arguing over what is most holy, to whom and who has the most rights to the holiness.
I am not sure I succeeded in much more than marvel at the ruins, churches and mosques.


Old City surrounded by newer city

Old City

Before walking into the Old Town, I remembered something my mum told me from her visit to Jerusalem many years ago.
“The smell. The smell of the city is just it’s entire own. Nothing compares.” 
The first paces around town seemed pretty trivial to me. I could smell gasoline, car exhaust, dog poop, pee, someone cooking something. Not really anything special. But as we walked further and further in to the Old City the smell changed. Now, a dry smell of old dusty rocks dominated. The endless shops with scarfs, jewelry and souvenirs sent out vibrant smells of incense. Shops with dry goods oozed of exotic spices, fruit stands smelled of ripe bananas and mangos, a turning sharwama dripping with grease. On top of that the people, the atmosphere, the noises, all combined created a special smell, a feeling, of being in a living, breathing organism called Jerusalem.

Market in Old City

Stand of Spices

 

Walking around as a non-religious Scandinavian posed a lot of clothes changing. My cold Viking blood overheats at 25 deg C, so walking around in +30 deg C is not possible if not in shorts and sleeveless top. My instinct tells me to get as much sun and vitamin D as possible so covering up is not second nature. However, going in churches, to the Wailing Wall and other holy places requires you to cover as a minimum knees and shoulders. My solution was a knee long flowy skirt that does a wonderful “Marilyn Monroe” imitation at every gust of wind and a Jordanian scarf tossed casually over the shoulders. So ready for the holy places!


Being so close to so many so religious people was very bizarre for me. To have people mumbling to themselves, rocking back and forth, crying over tombs of long lost Saints, put belongings on graves and in vaults to have them get blessed, falling to the knees before and alter, stop the business for 10 min while praying on a carpet, sticking secret notes to God in cracks. To me, so odd and bizarre behavior. To believe in stories and histories so old, and in places built centuries ago for who knows what purpose. To have so blind faith in old scripts, old ways and the one and only God dictating everything is just so far away from my own reality. In some weird way, it’s almost beautiful. But mostly I find it very, very stupid. But maybe I am not that different. My truth and my belief just lie in facts and science. In what I can see, touch, smell and feel. My holy scripts are the papers of scientific discoveries, my Saints are the animals, plants and humans in this world, and my church is the wilderness of nature and the depth of the sea. How you practice your truth and beliefs in this world is what it in the end comes down to.

Monastery

Church of the Holy Sepulchre

I could have spent more time exploring the crooked and cracked streets of Old City and visiting more holy places and admired the ability of ancient architects. This first little peak into history has for now satisfied me with the knowledge that Jerusalem is something else. In this hot and arid part of the world it exists in its own little isolated bobble in time and space.

Al-Aqsa Mosque
The Western Wall - Divided in a women and men section