Thursday, March 30, 2017

Good morning Science!

My morning began, as everybody's mornings should, with coffee.

However, from there, I doubt we had the same morning encounters.

Mine involved:
     -Robotic arms
     -Corrosive acids
     -5,000,000yo shells
...and...
     -Lasers!!!

Take a look with this upbeat (22sec) video:


Not a bad morning... 

#paleoceanography #chemistry #science #geochemistry #groundwater #ICPMS #ucsc #SlugScience

Monday, March 27, 2017

Ever heard of the coral holobiont?


Ever heard of the coral holobiont? Its a relatively new term that describes the coral system as a whole. This "whole" included the coral animal, its algal symbionts, bacteria, and fungi. Researchers came to realize that the coral organism is affected by the its community members. For example, bleaching can be caused, not only by the loss of algal symbionts due to temperature increase, but also due to bacterial infections, which similarly result in the breakdown of coral algae symbiosis. Furthermore, bacteria that were once harmlessly living on the coral polyps, feeding off a steady stream of mucous, can suddenly aggregate into these tissue eating mats. This occurs because bacteria act differently when their abundances increase above a certain threshold  (quorum sensing). Flesh eating bacteria are easily seen in diseases such as white or black band disease (A&C below).
Common coral diseases in the Caribbean. (A) Diploria strigosa with black band disease, (B) Dichocoenia stockesii with white plague, (C) Acropora cervicornis with white band and (D) Montastraea faveolata with yellow blotch syndrome. Photos E. Weil, from NOAA’s Center for Coastal Monitoring and Assessment Source: Reef Resilience 

Because of the multiplicity of interactions between corals and their constituents, we need to think about the entire community when we consider the coral organism's health. This isn't easy since most of these organisms are SMALL and SENSITIVE. Most bacteria from coral can't even be cultured in the lab. Neither can most of the symbionts and I haven't heard anything about culturing coral fungi, which is unfortunate since I've heard he's a Fun GUY (get it!). This means there is still a lot of room for new researchers (like you?) to help us understand the complexities of the coral holobiont. For now, I'm working hard on grasping how we use the coral holobiont DNA to understand the kinds of algal symbionts currently associated with the organism. Some of these symbionts may confer temperature resilience, although, this can come at a cost. Dr. Michael Stat and Dr. Ruth Gates wrote a great paper on the algal symbiont in clade D its freely accessible here.

In my next post I will tell you a little more about why this review paper is exciting, especially for the work I will be doing this summer.


Caffeine!

In a recent Environmental Health & Safety inspection, our lab was found to be non-compliant due to a lack of clearly-labeled 'emergency caffeine sources.'

To remedy this,

-A new DeLonghi espresso machine has been acquired

-Its Standard Operating Procedure (SOP) has been prominently displayed
-Students have been advised to brief themselves on the SOP in case they observe a labmate falling into a state of un-productivity

-A bag of espresso-grind coffee is now at the ready with clearly-labeled secondary containment
-Emergency caffeine sources are now clearly labeled in this artistic display of graduate student humor

Paytan Lab is now compliant.




#coffee #coffeeeee #LabSafety #SafetyFirst #Science

Wednesday, March 22, 2017

...and this is why science works

Scientists are not afraid to be wrong - this is an important distinction between this profession and many others. Some time may be lost going down paths whose results are maybe not as "exciting" as you wish they were. However, the beauty of science is that even a "less exciting" story is still... in the end... a story, which leads to a better understanding for those involved.

Image result for science


After discussing my proposed project in Israel months ago with my collaborators, we all thought it was a good idea to take a small sample-subset, analyze it in advance for barium (Ba) concentrations (which are a pretty good indicator of whether or not isotopic fractionation will occur), and then get some preliminary Ba-isotope data.

From this data subset, we hypothesized that we would see trends similar to other published findings in open ocean settings (such as this one here from Horner et al., 2015):
 Image result for horner et al 2015 barium

However, the lines came out a lot flatter than initially hypothesized with little surface variability. There are a few different reasons why this might be:
1) the Gulf of Eilat is just so oligotrophic that there is very little barite (BaSO4) formation occurring, which is what we generally think to be the primary driver of Ba fractionation in the surface ocean
2) the barite formation is confined to a much shallower surface zone (<200m), so increased depth resolution in the upper 200m is needed to elucidate the signature
3) the Gulf of Eilat's Ba chemistry may just be so driven by terrigenous dust inputs that the barite effect is really small and requires further work to deconvolve it from the dust

Either way, my initial hypothesis for how Ba isotopes would function in the Gulf of Eilat is so far not supported. Now it's time to determine what else is needed to truly reject the hypothesis, adjust the experimental parameters for alternative hypotheses, and evaluate their efficacy.

This is why I love science - its ability to change with new information.

Sunday, March 12, 2017

Corals!

I grew up in the Virgin Islands, on a small sail boat, surrounded by stunning coral reefs. One of my earlier memories was seeing these massive structures for the first time. I was stunned by all of the colors, fish, sea fans, and depth. If I am recalling this memory correctly, the site I was snorkeling is called the Indians. So I decided to check if there were any videos of the site on YouTube. If you watch this one. You'll probably realize, just as I did, that all of that color and diversity is gone. The site is pretty bland. Seeing this in person is disturbing to say the least. Unfortunately, the future for corals does not look that great. According to the 2008 World Coral Status report by Clive Wilkinson, 20% of coral area worldwide has already been lost.



The main mechanisms by which corals die stems from bleaching events. These events are triggered by sudden changes in the corals environment (mainly temperature) and results in the breakdown of the coral's symbiotic relationship with its algae. These algae are kicked out of the corals body and leave the translucent coral behind, exposing its bright white skeleton. Thus corals that loose their symbionts appear "bleached". Bleaching events can be massive - affecting up to 99% of corals on a reef! These corals essentially starve while they are bleached, since their symbionts are not there to make sugars for them. Starving corals are very susceptible to disease outbreaks and often die, although they can recover in seemingly rare instances.

Bleaching events are a global phenomenon and are decimating global reefscapes. The Great Barrier Reef in Australia, for example, just underwent one of the most devastating bleaching events. Just watch this video! You can see the bleaching from a plane!



Eilats reefs are different though... No mass bleaching events have ever been recorded. The hypothesized reason for this? Essentially an evolutionary bottleneck that caused corals to adapt to hot, salty temperatures really quickly (on geologic timescales, that is, <6,000 years). You can read about it here in this abstract. This makes Eilat a really interesting place to study coral reefs and their symbionts.



If you're in to Netflix (let's be honest - who isn't?), there's this really cool new documentary I'm dying to watch called Chasing Corals! It's coming out super soon and after I finally get to watch it, I'll undoubtedly post again to tell you what I thought of it. :-)



Stay tuned for more!

Stephan

Friday, March 10, 2017

Making Contacts, Getting Excited!


I have not made contact with the Timna team yet, but I had a wonderful Skype conversation last week with Beverly Goodman, a marine archaeologist who works at (among other places) a site called Caesarea. This is a (mostly) Roman site between Haifa and Tel Aviv.  Google says it was the second largest port in the ancient Mediterranean world.

I am hoping to work with Dr. Goodman to do some underwater video documentation and/or help edit some of their existing video and/or to help translate their 3D data into visualizations that tell a story.

One thing Dr. Goodman is working on is looking at how an ancient Roman sewer pipe at Caesarea connects to an ancient aqueduct. She is also looking at the tsunami stories of this ancient port city.  We discussed how 360 video, VR, AR could help to tell such a story.

Most of the ancient port at Caesarea is less than 30 feet underwater, which is well within the limits my beginner scuba skill level.  I am 3/4 of the way to my certification here on the Central Coast. It's been a bit slow going because we had to reschedule a couple of dives due to winter storms.   --and then there was a virulent campus bug going around and I got congested.  Don't attempt to dive with clogged ears.  Bad idea! But hopefully after finals, I will back in that 54 degree ocean of our, dreaming of the 82 degree seas of Israel!

This week I will speak with Dr. Goodman again, and hopefully reach the Timna Park team so that I can plan my time with them as I explore the archaeoacoustics of the ancient Egyptian copper mines and Hathor chapel there.


Stoked, Stressed, or both?

My first blog post!

Even though it’s only March, my projects are becoming better defined and I’m developing a relationship with my main collaborator, Eyal. It is somewhat challenging to clearly communicate through email, but I had a productive Skype call with Eyal. It turns out my proposal was a little too ambitious, so we honed in exactly what I will be doing whilst there. I just finished making my calendar and feel pretty good about it. 

I guess I should disclose that I have two main states: 1) stoked and 2) stressed. I feel I spend 95% of the time at state 1), state 2), or some combination of the two. 

I’m really stoked to have the opportunity to go to Israel since samples from a couple of my projects are from there. Also, I’m stoked because I will be able to work for two months straight without distractions and get a lot of data for my dissertation. I assume all graduate students potentially reading this are all familiar with the “Am I on track!?!” and “Do I have enough data??!??” anxiety hits – I think this trip is going to ease a lot of that for me. But…Who can say? Maybe nothing will work. After all, this is research J

I’m also really stoked about
-               snorkeling/diving in the Red Sea! The Paytan lab has plenty of divers, so I’ll have to ask them about what kind of camera is best for underwater photos.
-               going to Petra
-               learning more about Israeli culture
-               potentially surfing in Haifa – sadly peak season for waves is winter – but apparently there are some waves in the summer even
-               all of the food!

I’m stressed about
-               my projects not working
-               political climate
-               getting enough exercise during the trip – My productivity and mental health plummet if I don’t exercise. I even asked Eyal about this. He said there are gyms nearby. I’m not much of a runner, but I have a feeling that will be my activity of choice. Maybe I can kite/wind surf – I hear that’s big in Eilat… Or swim! We’ll see!
-               being homesick – I’ve become pretty attached to Santa Cruz. I’m sure I’ll be missing it.


In the next few days, I will be putting together my SOPs and list of supplies/instruments I will need for the trip. It’s hard to believe we leave in 4 months! So much to do until then!

Banana slugs are everywhere!

Have you ever taken a closer look at the Red Sea and its gulfs?
If so, maybe you've noticed before - but the Red Sea looks just like a banana slug, the mascot of UC Santa Cruz!
The two antennae = the Gulf of Suez and the Gulf of Aqaba (where we will be living this summer!)
Coincidence? ...I think not!


Friday, March 3, 2017

Bobbing for phytoplankton

People don't often complain that the game "bobbing for apples" is too easy. Every sport has its prodigies, though, so I have a new variant for advanced players I'd like you to consider:

Bobbing for Apples: Advanced
1. Find a group of participants who can survive a few minutes of swimming.
2. Pour a crate of about 100 apples into an Olympic-size swimming pool. Distribute apples randomly.
3. Place participants randomly in swimming pool, blindfolded.
4. At the signal of the judge, participants (still blindfolded) begin swimming.
5. The first participant who bites an apple without the use of hands is the winner.

Does this sound fun to you? Hopefully not. Given the choice, I certainly wouldn't participate. This isn't because I'm a poor swimmer -- I can dog paddle with the best -- it's because the game would be tiring, boring, frustrating, and dangerous. And when I say "dangerous", I don't mean the sort of thrilling and entertaining danger associated with, say, skydiving over a volcano or getting in a fistfight with a grizzly bear. This danger is mundane. At best, this activity sounds like how a water polo team with poor judgement (moral, practical, and aesthetic) might haze its new recruits.

All this being said, on the microscopic scale, this is how food for a lot of tiny creatures exists -- as little blobs of calories suspended in seawater. At the smallest level, the hunters are zooplankton, and their prey is phytoplankton. As such, the zooplankton have it even harder than the "bobbing for apples" participants. To better simulate their plight, consider the following rule adjustments to our game:

Bobbing for Apples: Zooplankton
To be played with the same rules as "Bobbing for Apples: Advanced", with the following amendments:
1. Instead of filling the pool with water, use a much more viscous fluid, such as glycerin or molasses.**
2. The participants must stay in the pool forever, eating only apples.
3. The winner, declared upon the death of all participants, is the one with the largest number of viable offspring.

As you might imagine, eons of evolution have given zooplankton a few tricks for catching their food. One trick of particular interest to me is that of particular zooplankton known as tintinnids. Instead of expending lots of energy swimming for their food, tintinnids have it delivered: they use a ring of beating cilia that creates a current in the surrounding water, funneling helpless phytoplankton into their oral cavity. Here's a video captured by Roi Holzman's lab at IUI showing this behavior:


(If the video doesn't load, try this link)

There are a number of questions we could ask at this point. Why does this motion of the cilia have a "funneling" effect? What is the best way that cilia can move to optimize prey capture? What effect do other parameters (mouth size, size of prey, ingestion rate, etc.) have on the feeding currents and particle capture?...

...we don't quite know! It's exciting! Well, for me anyway. Perhaps I'm unusual in that respect.

Anyway, that's what I'll be exploring this summer in a nutshell. Analytical models, hydrodynamics simulations, all that fun stuff. I'll keep you updated. For now, just remember that if you ever wind up bobbing for apples in a pool of molasses, don't bother kicking your feet.

-Steve

**This amendment might seem surprising -- after all, aren't zooplankton just swimming around in standard low-viscosity seawater? It turns out that the fluid mechanics of the motion of "swimmers" depends not only on the viscosity of the fluid, but also on things like how big the swimmer is and how fast the swimmer tends to move through the fluid (mathematically, this is where the Reynolds number becomes important). For this reason, if we wish to mimic the fluid mechanics of a small, slow swimmer in water by using a large, fast swimmer, we would need to crank up the viscosity of the fluid in order to compensate for this difference in scale.