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​BLOG BY GRACE C. YOUNG                                                                                                                                                             


2018 Updates

1/22/2018

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My Thesis: I've submitted my PhD thesis! Titled "Three Dimensional Modelling of Coral Reefs for Structural Complexity Analysis," the thesis examines the correlation between reef structural complexity and ecosystem health. 

For my thesis, I developed a new technique for creating and analyzing 3D models of underwater scenes using computer vision and machine learning. The methods are already being used by researchers in Indonesia, Madagascar, Bonaire, Cuba, Honduras, and the Maldives. I've published part of the research, and have five related publications nearing submission or under review. I hope the research will make a significant impact in our understanding of the ocean.

Ocean and Space Collaboration: I postponed submitting my thesis by two months to work in a NASA artificial intelligence accelerator last summer in California (blog post here). It was a chance to apply my knowledge of 3D modeling underwater ocean scenes to the challenge of 3D modelling near-earth asteroids. It was a fantastic opportunity that not only augmented the last chapter of my PhD thesis, but also allowed me to grow personally and professionally.

​Our team of four engineers at NASA's Frontier Development Lab used a range of machine learning techniques to automate asteroid 3D modelling. My team's results were well-received by NASA's Planetary Defense community and the tool my team developed will be implemented this year at the Arecibo Observatory to help track near-earth asteroids.

Upcoming Events: While waiting for my PhD defense in March or April, I've committed to a few speaking events, listed below.  
  • Jan 27-31 - NatGeo in London: I'll be attending NatGeo's first-ever London Explorer’s Festival. I'll share updates about current and upcoming projects with the NatGeo community, and we'll celebrate with Jane Goodall the release of her critically-acclaimed film (read more here & find a screening near you).
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Washington, DC, April 10 at 7:30PM^
​General Admission
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Washington, DC, April 10 10AM^ Student Matinee
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Celebrating thesis submission.^
  • Feb 3 - CERN Speech in Geneva: I’ll be speaking at CERN in Geneva, Switzerland, about the “CERN for the Ocean” idea I presented in this 2015 TIME op-ed. The idea that has morphed into the a broader “CERN for the Planet.” More about my connection to CERN in previous blog post "Return to CERN." 
  • Feb 6-8 - Marine Technology Society presentations in New Orleans: I’ll be speaking in New Orleans at the Underwater Interventions conference hosted by the Marine Technology Society. With the Pisces VI submarine team, we will share updates from the build. Additionally, I'll present my thesis work on 3D modelling underwater scenes. I've attended this conference almost every year since I was 19! 
  • Feb 13 - Classroom Outreach: I’ll be hosting a live classroom session with NatGeo’s "Exploring By the Seat of Your Pants." Any classroom can sign up for free here! This session will be from our submarine workshop in Salina, Kansas, with the Pisces VI deep-sea submarine. Follow that project on Facebook and Instagram; also previous blog post "Submarines in Kansas? Yes! Pisces VI to Bring Deep Sea Research to the Masses."
  • Feb 26-27 - MIT Media Lab: I'm thrilled that Katy Croff Bell is launching the Open Ocean Initiative at MIT Media Lab. It will "design and deploy new ways to understand the ocean and connect people to it, empowering a global community of explorers." I'll be at one of the first events "Here Be Dragons" in Boston this February. Most of the talks will be live streamed from MIT or the New England Aquarium. More information here.
  • April 10 - Join me for "Extreme Oceans" Presentations in DC (a Student Matinee at 10AM,  and a General Admission at 7:30PM): I’ll be speaking at NatGeo Headquarters in Washington D.C. about why I care so much about the ocean, how my interests developed, and more broadly about the future of our ocean, the technology and policies we need, and how everyone can get involved. I'll give both a students-only matinee and an evening talk open to the public. Tickets are available here through NatGeo.  Friend Anand Varma (who did the awesome slo-mo story of on hummingbirds you might've seen!) will be speaking a few days later on April 13. 
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NatIONAL GEOGRAPHIC Interview About conducting Research, Living Underwater, and STAYING CONNECTED DURING Fieldwork

11/20/2017

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I recently did a phone interview with National Geographic's Jonathan Manning. It's now featured on the front page of National Georaphic's  UK website. Excerpts below and full interview here. 
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What are you currently exploring?
I’m working on several projects while finishing up my PhD at Oxford. My thesis is focused on 3D mapping coral reefs and the correlation between reef structure and the health of its ecosystem. I’m monitoring the structural complexity of the reef, how it changes over time and how fish interact with the 3D structure. It’s an inter-disciplinary project involving zoology and engineering that requires a lot of time underwater studying the reefs off the coast of Honduras. I’m also helping to rebuild a deep-sea research sub, Pisces VI, that will allow us to discover more deep-sea species and better understand how ocean ecosystems function. Finally, I’ve just started a project developing new technology to enable us to genetically analyse sea creatures in their natural environment; this project is in its very early stages though.

What’s so fascinating about coral reefs?
Coral reefs are the mega-cities of the ocean. They host as much as 25% of all marine life, but they cover less than 1% of the ocean floor. One of the reasons they are able to do that is because they have this gorgeous structural complexity that creates niches for species to hide from predators or weather storms and a great surface area for a diversity of creatures to feed on.
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Grace dances outside Aquarius, her underwater home for 15 days during Mission 31. Photo: Fabien Cousteau - Mission 31.
How much of your study involves fieldwork?
I spend three months of the year doing fieldwork and the rest doing data analysis or developing testing technologies here in Oxford.

Where do you conduct your fieldwork?
My doctoral thesis is based on a fairly remote island called Utila, in the Caribbean, a couple of hours by boat from mainland Honduras. There are only about 4,000 people who live there, and there’s just one main road on the island – you could take a golf buggy around the island in a day. We have a field station there that’s been operational for about a decade, operated by a conservation group, Operation Wallacea. We chose the site because it’s been monitored for several years so we have a baseline. 

It sounds like paradise!
Not quite - it’s like a glorified weight loss camp! We’re busy every day. I’m up at 7am, I grab breakfast of rice and beans at the dive centre, then put on dive gear and do three or four dives per day, each about an hour underwater. I never dive alone. I always have at least one dive buddy, usually a research assistant. We set up experiments and collect data. Last summer I did a lot of heavy lifting. We had a series of concrete tiles underwater that we were growing coral on – we had to put them down and then bring them back to the surface. Each tile weighed 2.5 kilograms (5 pounds) and there were 200 of them – that’s half a ton! I come back from fieldwork in the best shape of my life!
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Grace enjoys a cup of tea with Fabien Cousteau, while living underwater for more than a fortnight.
How do you keep in touch with friends and family when you’re on Utila?
It’s not easy. I’m often working in areas with limited to no internet or mail services, so the typical means of communicating with loved ones aren’t available. Recently I’ve started to write and exchange a bunch of letters with close friends before I leave. We can read them each week I’m away and so stay in each other’s thoughts. I also periodically treat myself to an internet connection – although this sometimes requires literally walking across the island. That’s a serious commitment to sending a text message!

Do you miss important news?
I remember coming out of the water after a dive and someone told us that Britain had left the EU. I wasn’t sure I had heard right, but I had several more hours of diving that day, so I couldn’t confirm it. Because the internet is so spotty on the island, we rely on word of mouth for news. You cannot surf the news as normal. When I’m away people joke, “have you been under a rock?,” and I reply, “no, I’ve been underwater.” On the plus side, being offline and away from everything allows me to really focus on my research. Also, I try to compensate for the isolation by reading more books and longer form works.

Have you even been in danger?
People often ask me this – weren’t you scared of living underwater? Of diving with sharks? Of sailing across the ocean? Of diving at night? The list goes on; but really, everything I’ve done is safe. I wouldn’t do it otherwise. Before an expedition we do risk assessments to think through every emergency situation and determine how we should respond. The danger really isn’t from sea creatures so much as it’s from carelessness,. Overall I’m probably in more danger walking across the street in Oxford.

Where would you most like to be right now?
I’m always happiest on or in the water; but I try to live in the moment, so I’m very happy here in Oxford – although I miss the ocean.
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Which luxuries do you sneak into your luggage before every trip?
I always wear my Doxa dive watch, which I got on a previous expedition, called Mission 31, when we lived underwater for 15 days in the Aquarius habitat. The watch has an iconic orange face.
... read the rest at ​http://www.nationalgeographic.co.uk/environment-and-conservation/2017/11/underwater-explorer

Other News

I'm in the December issue of National Geographic Magazine! Did you read it?
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Summer at NASA - Update

8/4/2017

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So far so good! My previous blog post explains why I'm at NASA this summer. In short, I'm still 'Team Ocean' (of course!), but the 3D shape modelling techniques developed for my PhD on coral reefs have direct application for NASA's research on near-Earth asteroids (and vise versa). It's been a fantastic collaboration. Here are more details about what we're doing and why. 

What We'RE Doing and Why 

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<- Explaining our work during a Facebook live event for SETI (here on Facebook; it's been viewed by >30k!). 
NASA's Frontier Development Lab (FDL) is an experimental tool in NASA’s innovation portfolio that emphasizes artificial intelligence, inter-disciplinary approaches, rapid iteration, and teamwork to produce significant breakthroughs useful to the space program.

​This summer, four of us at NASA FDL are creating 3D models of asteroids. Our core team comprises two planetary scientists (Agata Rozek and Sean Marshall), two machine learning engineers (Adam Cobb and me), plus mentors from both disciplines (Chedy Raissi,  Michael Busch,  and Yarin Gal). We’re creating the 3D models from radar data. It's a difficult computational problem, but knowing an asteroid’s 3D shape helps us predict its future trajectory (/whether it will collide with Earth!). 

The formal introduction to our problem reads as follows: 
​Delay-Doppler radar imaging is a powerful technique to characterize the trajectories, shapes, and spin states of near-Earth asteroids and has yielded detailed models of dozens of objects. Since the 1990s, delay-Doppler images have been analyzed using the SHAPE software developed originally by R. S. Hudson and S. J. Ostro [1, 2]. SHAPE normally performs sequential single-parameter fitting. Recently, multiple-parameter fitting algorithms have been shown to more efficiently invert delay-Doppler data sets, thus decreasing runtime while improving accuracy [3]. However, reconstructing asteroid shapes and spins from radar data is still, like many inverse problems, a computationally intensive task that requires extensive human oversight. The FDL 2016 team explored two new techniques to better automate delay-Doppler shape modeling: Bayesian optimization [4] and deep generative models [5]. The FDL 2017 team is refining that work and exploring new directions for more quickly and accurately generating 3D models of near-Earth asteroids from delay-Doppler images.
It took me a bit to understand exactly what our goals and motivations were. The most common questions my friends ask are, “What are you doing?” and “Why?” My short answer: We're generating 3D models of asteroids from radar data so that we can better determine asteroids' physical properties and orbital trajectories. There are over 16,000 known near-Earth objects, and on average 35 new ones each week. It's too much data to keep up with without sophisticated data analysis techniques, so we're  using machine learning to speed up and automate the process of generating 3D models from radar data of asteroids.

Still #TeamOcean

I'm also interested in the task of 3D modelling asteroids because the techniques can be applied to 3D modelling coral reefs, the topic of my thesis, as further discussed in my first post about NASA.

Preliminary Results

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Result 1A: Delay-Dopler images (example above) are converted into 3D models of asteroids (example at right).
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Result 1B: Last year a team trained a neural network to generate 3D asteroid shapes in the form of voxels (cube-like 3D pixels). We've developed triangular meshes from those voxels, and have smoothed the 3D shapes so that they better resemble asteroids. We'll be feeding a set of synthetic radar shapes into a deep neural network to train the network. For more details, stay tuned for our presentation on August 17th in Silicon Valley. ​​​

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Result 2: We wrote a script that that finds signals in sets of delay-Doppler radar images. This quickens pre-processing of the data. The script intelligently masks the signal from the noise in an image using a density-based clustering (DBSCAN) algorithm.

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Result 3: We also wrote a script that estimates the spin state of an asteroid from available data. That data can be radar data, optical or light curve data, or any of the input sources used by existing 3D modeling software for asteroids called SHAPE. It quickly and efficiently estimates spin states by performing Bayesian optimization on a spherical coordinate system. Already processing time has gone down from 3 days to 4 hours (and getting faster!).
More details will be in our final presentation and report at the end of the summer. Register here if you'd like to attend our final presentation in Santa Clara, California. 

References: 
​[1] R. Scott Hudson. Three-dimensional reconstruction of asteroids from radar observations. Remote Sensing Reviews 8, 195–203, 1993.
[2] Christopher Magri, Michael C. Nolan, Steven J. Ostro, and Jon D. Giorgini. A radar survey of main-belt asteroids: Arecibo observations of 55 objects during 1999-2003. Icarus 186, 126–151, 2007. 
[3] Adam H. Greenberg and Jean-Luc Margot. Improved algorithms for radar-based reconstruction of asteroid shapes. The Astronomical Journal 150(4), 114, 2015. 
[4] Jonas Mockus. Bayesian Heuristic Approach to Discrete and Global Optimization: Algorithms, Visualization, Software, and Applications. Springer-Verlag, Berlin, Heidelberg, 2010. 
[5] Ruslan Salakhutdinov. Learning deep generative models. Annual Review of Statistics and Its Applications 2, 361–385, 2015. 
​[6] Shane Carr, Roman Garnett, and Cynthia Lo. BASC: applying Bayesian optimization to the search for global minima on potential energy surfaces. International Conference on Machine Learning. 2016.
This post is modified from the original published on the NASA FDL page (here). All work was developed while at NASA Frontier Development Lab, working with Agata Rozek, Sean Marshall, Adam Cobb, Justin Havlovitz, Chedy Raissi,  Michael Busch,  and Yarin Gal.  

UPDATE - 12 Sept 17

My colleague Adam just posted his perspective on the project. Read his blog post here. 

Update - 20 Nov 17

The video of our final presentation at Intel Headquarters is live! It's on YouTube at this link.
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Update - Jan 2018

The results from our team of four engineers and scientists were well-received by NASA's Planetary Defense Community. The tool we developed will be implemented this year at the Arecibo Observatory to help track near-earth asteroids.

Related blog posts:
  • Looking up! NASA this Summer
  • Aquarius Day 3: Met an Astronaut Underwater
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LOOKING UPWARDS THIS SUMMER -- INVITE TO NASA

5/25/2017

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Excited to announce that I’ve been offered a research position this summer at NASA’s Frontier Development Lab in Mountain View, CA. I’ll be working alongside other scientists and engineers for eight weeks in an intensive research accelerator focused on artificial intelligence.
Hosted by the SETI Institute and NASA Ames and supported by leaders in AI from the private sector, such as IBM, Nvidia, Autodesk and Miso Technologies, FDL brings together teams of experts in the physical sciences and specialists in data science and machine learning for an intense 8-week concentrated study on topics important to NASA – and to humanity’s future. The format encourages rapid iteration and prototyping to create outputs with meaningful application, papers and conference posters.
They've asked me to develop a project with cohorts on near-earth object 3D shape modelling and lunar water detection, topics that directly relate to my thesis (minus the "lunar" part and replace "near-earth" with "underwater" of course!). It's a fantastic opportunity to develop skills and learn from NASA in ways that will not only further develop our underwater 3D modelling techniques, but also vise versa; they'll learn from our research techniques. 
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Image: G. Young Credit Mission 31.

Still Team Ocean

Ocean and space are commonly pitted against each other – upward vs downward – astronaut vs aquanaut, etc. ​
Fabien Cousteau and Liz Magee from Mission 31 recently debated in a Science Throwdown: Space vs. Sea at the American Museum of Natural History, and Nat Geo 2011 Explorer of the Year Kenny Broad plans to highlight the topic in his Red Planet vs Blue Planet session at the National Geographic Explorer’s Festival this June.

​I delve into the debate’s history in my undergraduate thesis Missiles and Misconceptions: Why We Know More About the Dark Side of the Moon Than the Depths of the Ocean, TEDx Talk Why We Know More About the Moon Than the Depths of the Ocean, and in an interview for an upcoming PBS documentary based on Ben Hellwarth’s awesome book SEALAB.
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It’s not an either-or debate, however. We can explore both.
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I’m looking forward to this summer opportunity at NASA for a number of reasons. I’m eager to learn from NASA methods that will enhance our underwater 3D modeling techniques while sharing what we’ve learned underwater. The experience will also provide another perspective on how public-private partnerships can work effectively to achieve defined research objectives. I believe public-private partnerships like NASA FDL and what I observed at CERN OpenLab, are the key to tackling our most urgent  ocean research objectives---a vision I outlined in my 2015 TIME op-ed. Finally, I’m excited to spend weekends diving, surfing, and reuniting with West Coast friends.
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Image: G. Young credit Mission 31

Many astronauts are also aquanauts, but most people don’t realize more people have been to space than have lived underwater! Several acquaintances work in both arenas: Pisces VI submarine owner Scott Waters is also on a space advisory board. FDL founding member, Jordan McRae, invented OctoTalk, a system for divers to transmit voice communications underwater. Jonathan Knowles, who is involved with FDL through Autodesk, also advises The Hydrous, an organization that 3D models corals around the world.
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That said, I’m committed to Team Ocean. I’m personally drawn to water, a connection many humans have (see Wallace Nichols' book Blue Mind: The Surprising Science That Shows How Being Near, In, On, or Under Water Can Make You Happier, Healthier, More Connected, and Better at What You Do.).

Moreover, engineering-wise, while space may seem more exotic, I’d argue the ocean, particularly the deep ocean, is a more challenging work environment considering that E&M waves, upon which wifi, GPS, and many modern innovations are based, do not work, and salt water kills electronics. We’re forced to innovate.

(Thanks Somerville (Oxford) for the article with video!)
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EXPEDITION, HONDURAN BAY ISLAND 

6/28/2016

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I'm once again on the island of Utila conducting research with Operation Wallacea. I'm leading a team of four students 3D mapping the coral reefs here and retrieving 3D printed artificial reefs we placed last year. Our studies will help reveal how how reef structure, or architectural  complexity, affects  marine communities. My upcoming papers and thesis will be on the topic! Stay tuned! 
3-legged turtle swims past
Stuck in tropical storm
Boating past small island
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Talk At Oxford Underwater Exploration Group

5/9/2016

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Yesterday Dominic Andradi-Brown and I presented at the annual dinner of the Oxford University Underwater Exploration Group (OUUEG). We talked broadly about using technology to explore coral reefs, and gave examples from our work together on rebreathers in the Caribbean and Red Sea. We also talked about our separate expeditions, including Dom's in Indonesia with Operation Wallacea and mine in the Keys with Mission 31 and in Hawaii with NOAA's Pacific Islands Fisheries Science Center. 

UPCOMING TALK

I'll also be talking at Somerville College in Oxford as part of their "Will Power Lunch" on May 21st. 
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... and again at Somerville College, on May 23, as part of a series on emotional well-being in research and fieldwork. Please message if you'd like more details. 
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BAY ISLANDS

7/27/2015

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I'm currently on Utila, an island off Honduras, collecting data. I'm working with Operation Wallacea and two other graduate students from Oxford. Regular updates are on my Instagram and our expedition Facebook page, "Thinking Deep."
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Right to left that's Dom, Jack and me, the Oxford underwater research team.
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PHOTOS FROM ISLAND EXPEDITION 

4/9/2015

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The last two months my research team at Oxford and I have been exploring mesophotic reefs using Hollis Prism 2 rebreathers. More information in this blog post -- "Diving Deeper and Longer to Study Never Before Seen Coral Reefs" and our Facebook page -- "Thinking Deep."
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DIVING LONGER & DEEPER WITHOUT BUBBLES TO STUDY NEVER BEFORE SEEN CORAL REEFS

3/11/2015

 

REBREATHER TRAINING: BEYOND TRADITIONAL SCUBA

The past weeks I've been learning to rebreather dive with two other Oxford PhD students. The rebreathers allow us to study reefs below traditional SCUBA depth limits (up to 120m/400ft). They also scare away fewer fish than traditional SCUBA because they don't produce bubbles. The concept is that on a rebreather you're essentially breathing the same breath over and over; when you exhale CO2 is removed and oxygen added. The only caveat is that the units are more mechanically complex than normal SCUBA rigs and therefore require more training and skill. 
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Resurfaced from our first rebreather dive; from left to right, our instructor Elliott Jessup, Jack Laverik (fellow PhD student), me, and Dom Adriadi-Brown (fellow PhD student). 
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Our team is keeping up a Facebook page. "Like" for updates. 
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Learning to use Google Ocean "Street" view.
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Filling oxygen cylinders; getting ready for a dive.

A LITTLE REBREATHER HISTORY

Rebreather technology has been around more than a decade, but they are only recently becoming more widely used and accepted in the scientific and recreational diving communities. Statistically, diving a rebreather is more dangerous than diving SCUBA. Accidents are all linked to user error, however, apart from a few truly freak accidents. If a diver is well trained, thoroughly inspects and maintains her unit, and follows a conservative dive plan, the rebreather diving is extremely safe and greatly benefits research. They allow us to dive to greater depths for longer periods of time and without bubbles that disturb marine life.  

WHAT & WHERE

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One of the research questions we are looking into is how deep reefs may (or may not be) sheltering some corals from the effects of climate change and fishing. More on that question in this PBS article. 

We are training off the island of Utila, which is the site of my dive buddies' (Dom and Jack's) PhD experiments. They have a close relationship with the dive center here as they help run a program for marine biology students here on the summers. The reefs here are fairly healthy and can be reached without expensive boat trips, which is somewhat rare and helps keep research costs low. To top it off, Utila is a gorgeous Caribbean island! 
The pictures with captions in the slide show below illustrate some of our adventures so far, including learning to use the Google Street "Ocean" View camera. 

UPCOMING ADVENTURES

2/5/2015

 
Next week I'll be temporarily leaving the comfort of Oxford for an exciting round of adventures. It starts in New Orleans, for the Underwater Interventions conference sponsored by the Marine Technology Society, where I'm giving talks on the ultra-slow motion underwater camera from Mission 31 and the stereo-camera system for monitoring fish from NOAA. From there, a friend and I will road trip through the alligator-infested swamps of Louisiana for a few days before flying to Washington DC to see family and move the exhibit of ultra-slow motion underwater photography from MIT to its next stop, The Potomac School in McLean, VA. I'll then rendezvous with our Oxford research team in Miami, where fellow aquanaut Adam Zenone has kindly been accepting our shipments of research equipment, before heading to Utila, Honduras, where we'll spend four weeks training on rebreathers and flying the openROV over mesophotic coral reefs. And finally, back to the comfort of Oxford! 

"I DARE you, while there is still time, to have a MAGNIFICENT obsession." William Danforth

A ship is safe in harbor, but that's not what ships are for.

CHECK OUT FELLOW PHD STUDENT'S WORK

1/20/2015

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Another PhD student in my group needs 18 months to finish analyzing an enormous set of data he has collected on coral reefs. I just highlighted his work and Crowdfunder campaign on the Act Now page; learn more and support if you can! His work is fascinating and he's happy to reach out to groups who want to learn more about coral. 
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    Grace Young is an MIT ocean engineer, aquanaut, and scientist/engineer with Cousteau's Mission 31. She's currently a PhD student at University of Oxford, chief scientist for the Pisces VI deepsea submarine, and a National Geographic Emerging Explorer. 

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