Open source. Open science. Open Ocean. Oceanography for Everyone and the OpenCTD

Oceanography for EveryoneJune 24, 2016

Andrew compares the OpenCTD readout to a hand refractometer, because apparently he's a hipster ecologist.

Andrew compares the OpenCTD readout to a hand refractometer, because apparently he’s a hipster ecologist.

Nearly four years ago, Kersey Sturdivant and I launched a bold, ambitious, and, frankly, naive crowdfunding initiative to build the first low-cost, open-source CTD, a core scientific instrument that measures salinity, temperature, and depth in a water column. It was a dream born from the frustration of declining science funding, the expense of scientific equipment, and the promise of the Maker movement. After thousands of hours spent learning the skills necessary to build these devices, hundreds of conversations with experts, collaborators, and potential users around the world, dozens of iterations (some transformed into full prototypes, others that exist solely as software), and one research cruise on Lake Superior to test the housing and depth and temperature probes, the OpenCTD has arrived.

Kersey strike a pose while deploying an OpenCTD in our local estuary.

Kersey strikes a pose while deploying an OpenCTD in our local estuary.

Over the last week, Kersey and I have been hard at work building a battery of CTDs while methodically documenting the construction process. You can watch the event unfurl on the #HackTheOcean hashtag. We now have three new CTDs ready to be distributed to collaborators at various institutions for more field tests and, in particular, to assess the precision of three different conductivity probes, all of which have been calibrated and validated here, in Virginia.

OpenCTD versus commercial CTD temperature and depth test. Conductivity test are occurring this summer, but initial surveys indicated no significant deviation from commercial instruments (indeed, we’re even using a commercial conductivity circuit that has been thoroughly tested in other environmental monitoring contexts.)

Now, finally, after 4 years of challenges and opportunities, of redesigns, re-education, and re-development, it’s time for you to join our open-source community of Citizen Oceanographers and build your own OpenCTD!

We’ve hosted the entire build guide, as well as the software, 3D printer files, support documentation, and raw data from our first research cruise in the Oceanography for Everyone GitHub repository, where you can also find guides and designs for the BeagleBox field computer and the Niskin3D 3D-printable Niskin bottle. 3D print files are also available on Thingiverse, if you’re more comfortable with that platform. We’ve also gone out of our way to make the build as simple as possible. You’ll need to learn basic programming and electronics, but the technical aspects of building your own CTD shouldn’t be a barrier to entry.

Over these four years, the OpenCTD has grown from a single project to a community of citizen oceanographers committed to making the tools needed to study the oceans as accessible as possible. As my friend and colleague Eric Stackpole said upon launching the first OpenROV kickstarter:

“Ocean exploration shouldn’t require a research grant, it should require curiosity.”


Since launching, numerous people have asked us if we can build an OpenCTD for them. We are not really set up to be a manufacturer of CTDs, however, get in touch with either me ([email protected]) or Kersey ([email protected]) and we can talk about holding an OpenCTD training workshop with your institution or organization.

Help crowdfund shark research: will the weasel shark disappear before we know it?

marine science, Natural Science, Science, sharks

Manuel_Dureuil_BWManuel Dureuil is a Ph.D. candidate whose research focuses on the conservation ecology of sharks. He did both, his Bachelor and Master thesis, in the field of shark conservation at the University of Marburg and Kiel in Germany. His main interest are spatial ecology and data-limited assessment approaches to form a scientific basis for a more comprehensive protection of sharks. A species with particular focus of his research is the Atlantic weasel shark, which is only found in West Africa. Sharks in this area are among the least researched yet most threatened by illegal and unregulated fishing. The weasel shark fulfills all criteria to be considered data-limited: there is no population assessment, no information on its spatial ecology and almost no information on its biology. Manuel is raising funds till the 9th of July as part of The Experiment’s Sharks Grant Challenge, to start a weasel shark project in Cabo Verde, West Africa. Using the weasel shark as an umbrella species the researchers also hope to create awareness for sharks in this region in general, on a national and international level.

The remote island nation of Cabo Verde holds one of the last remaining hotspots for sharks in the entire North Atlantic Ocean and therefore could offer some degree of protection from the ongoing decline in shark populations. This is particularly important for locally endemic species which only occur in this area, such as the Atlantic weasel shark. We know almost nothing about this species and accordingly it is listed as ‘data deficient’ on the IUCN Red List. However, the little we know suggest that this shark is vulnerable to overfishing, making the protection of important habitats (such as nursery grounds) crucial for healthy populations and preventing extinction.

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Help crowdfund shark research: Jaws, lost sharks, and the legacy of Peter Benchley

marine science, Natural Science, Science, sharksJune 22, 2016

1-Head shot for bio_Dave SFS Article pic_Photo by DA EbertDavid Ebert has been researching sharks and their relatives (the rays, skates, and ghost sharks) around the world for more than three decades focusing his research on the biology, ecology and systematics of this enigmatic fish group. His current research efforts are focused on finding, documenting, and bring awareness to the world’s “lost sharks”. If you would like to learn more please see our crowd funding project “Looking for Lost Sharks: An Exploration of Discovery through the Western Indian Ocean” and consider making a donation. The more we raise, the more sharks we can name and the more schools we will be able to reach.

Jaws, the mere mention of the movie conjures up images of a large triangular fin cutting through the water, beneath it a large fearsome-looking toothy shark swimming with a sense of authority, a purpose. One of the movie’s trailers at the time hyped the fact that this was a mindless eating machine!

I recall seeing the movie Jaws in the theater for the first time during my high school days in the summer of 1975.  It was the first big summer blockbuster film, it was something new to audiences, and certainly new to me. Prior to the film’s release people generally did not anticipate such great summertime entertainment from movies like Jaws and subsequently Star Wars (released in 1977).  These were fun movies to see with your friends and spend an afternoon or evening afterwards talking about certain scenes or dialog from the movie, “You’re gonna need a bigger boat”; remember this was back in the pre-iPhone, Facebook, Twitter, social media era when kids actually spent time together talking with each other, without the aid of electronic devices and no texting!

The movie as an ancillary and an unintended consequence brought a lot of attention to sharks, both good and not so good. Shark attacks that were of minimal media attention became big news stories, catching big sharks became a sport and shark diving became popular; all of this after the movie’s release. A few high profile shark attacks, one in particular in Monterey that made international news, only further fueled the public’s fascination and fear of sharks. Just going into the water suddenly became an adventure, with the prospects (however unlikely) that one may see a shark. It certainly put the public’s awareness of sharks in their conscience.

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Reflections on the Boundary of Science and Policy

#SciComm, Conservation, Science Life, Social ScienceJune 20, 2016

People have dedicated their careers and spilled much ink on bettering relations across the science – policy divide. In recent years, whole institutions have sprung up in order to better communicate and work across this boundary, the kind of institution formally called a boundary organization. In short, the people who work at such places must know the language and culture of both sides, be able to navigate around the sensitivities of each, and serve as a trusted person in moving a conversation along. These people are often called “honest brokers” because of the importance of the trust they must gain and hold. As someone who’s now working on the boundary for a number of years in the marine conservation world, I have some reflections of how exactly that role is not so simple. Hopefully my top 10 reflections will be helpful in building the next generation of boundary spanners. (more…)

Life in the Ithilien ranger service

Field notes from Fantasy, UncategorizedJune 19, 2016

People call them the “Dead Marshes”, but that couldn’t be further from the truth. The marshes are in fact incredibly biodiverse and productive. Admittedly that productivity has a lot to do with the slow decomposition of the corpses of men and elves, but they are productive nonetheless. The marsh vegetation also plays an important part in detoxifying the ecosystem. There is a slight problem with the level of mithril contamination in the marshes, but there are several marsh plants that sequester this trace element.

 Illithien ranger2

The marshes are also important sinks for carbon. Climate change is increasingly a concern in Middle Earth, what with the dramatic rise in dragon-related emissions and the felling and burning of Fangorn Forest, not to mention the carbon dioxide plume from Mount Doom.

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Did monster hunters find a 120 meter long giant squid on google maps?

A Renewed Sense of WonderJune 17, 2016

oopsNo. No they did not.

I awoke this morning to a delightful flood of emails in my inbox pointing to this article: Has a KRAKEN been spotted on Google Earth? Monster hunters claim to have found 120m long giant squid-like creatureIn short, while exploring the area around Deception Island on Google Earth, some well-known anomaly hunters found a weird thing.

Google maps is full of weird things. The planet is full of weird things. Weird things are awesome.

Rather than dig just a little bit deeper, they went on to wax poetic about giant squids, busted out some measurement tools to determine that it was 120m long, and promptly alerted the press. Also, another anomaly hunter says it’s a UFO.

If, however, they had pulled up a nautical chart, they would have realized that this is Sail Rock, a well mapped outcropping that, from the sea, looks a bit like a ship under sail.

Sail Rock (http://www.scielo.cl/scielo.php?pid=S0718-71062013000100001&script=sci_arttext)

Sail Rock (http://www.scielo.cl/scielo.php?pid=S0718-71062013000100001&script=sci_arttext)

Update: Since I can’t find an easily-accessible nautical chart of the island online, here’s a high resolution scan showing the rock and its relation to Deception Island. 

Deception Island to King George Island

Sorry, folks, it ain’t a 120 meter long Kraken or an Underwater UFO. It’s a rock.

#JacquesWeek 2016 Official Schedule

EducationJune 16, 2016

“The sea, once it casts its spell, holds one in its net of wonder forever.”

Jacques Yves Cousteau

Summer is here, and with it comes the perennial ocean explosion that is Shark Week. Last year, in response to Shark Week burn out (heck, David and I even published a paper on it) and being tired of becoming the saltiest of wet blankets during a week where people are excited about the oceans, we launched #JacquesWeek! #JacquesWeek is an online alternative the Shark Week. We sourced and screened Jacques Cousteau documentaries from the early years all the way through his later works and provide context and discussion from an array of marine scientists and explorers.

#JacquesWeek is back!

From June 26 to July 1, we’ll feature classic Cousteau films, hold Twitter discussions, and host a few hangouts with experts to discuss these films and help put them into context. As with last year, we will try to provide as many free options as possible (due to some very complex issues surrounding copyright, the Cousteau estate, a production company that no longer exists, and some fascinating interpersonal politics, many of Cousteau’s earlier films are de facto public domain) but we will also be drawing from his later series: The Jacques Cousteau Odyssey, Jacques Cousteau Pacific Explorations and Jacques Cousteau River Explorations which you will have to track down on DVD (but don’t worry, alternate suggestions are also provided)

Are you ready for adventure?

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Help crowdfund shark research: bycatch reduction with the loopy leader

fisheries, marine science, Natural Science, Science, sharksJune 15, 2016

GlennDr. Glenn R. Parsons is a 30 year veteran in the battle against University Administrators, bean-counting bureaucrats, and disinterested students (i.e. he is a Professor at Ole Miss). In his spare time he conducts research work on fish physiology and ecology and has published many papers on shark biology, primarily Gulf of Mexico species. He is author of the seminal book on sharks of the Gulf of Mexico entitled “Sharks, Skates and Rays of the Gulf of Mexico” and a popular novel entitled “Cherokee Summer” that could have been on the New York Times best seller list (if only it was better written and was backed by a high-powered agent like John Grisham’s). He received his PhD from the University of South Florida, School of Marine Science, MS from the University of South Alabama and BS from the University of Alabama. He was a DISL Marine Research Fellow, a Gulf Research Council Research Fellow, and a winner of a World Wildlife Fund, Smartgear Competition (for his bycatch research).

Folks, The world has witnessed an unparalleled decline in sharks that began about 30 years ago and has continued to the present. While the explanations for this decline are varied, scientists are in agreement that “bycatch” during fishing is one of the problems. Bycatch is the un-intended capture of non-target species during fishing. For example, commercial fishing for tuna and swordfish results in the capture of many sharks. The World Wildlife Fund estimates that 50,000,000 sharks are taken as bycatch during commercial fishing. Unfortunately, many of these sharks do not survive the stress of capture (a topic that my lab has researched for many years). Fishers do not want these sharks (they are dangerous to handle and they damage fishing gear) and they would welcome new developments that would reduce or eliminate shark capture.

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Help crowdfund shark research! Always chew your food – how freshwater stingrays gnaw on prey.

Natural Science, ScienceJune 14, 2016

MattMatt Kolmann is a PhD candidate whose research program is at the interface of evolution, comparative anatomy, and biomechanics. He completed his Master’s degree at Florida State University with Dr. Dean Grubbs on the feeding biomechanics and fisheries ecology of cownose rays, a purported pest on commercial shellfish. During this process he developed a love of field work, and since then has collected rays and other fishes on expeditions across South and Central America with the Royal Ontario Museum. His PhD research investigates the evolution of biodiversity using South American freshwater stingrays as a model system. The number of different feeding niches these stingrays occupy is astounding, and Matt is using gene-sequencing, comparative phylogenetic methods, and biomechanical modeling to characterize the evolutionary processes underlying this biodiversity. From June 8th through the end of Shark Week, he will be raising funds to delve more deeply into the evolution of feeding behavior in freshwater rays – specifically investigating whether freshwater rays ‘chew’ tough prey like insects in a manner comparable to mammals. Follow him on twitter! 

What role does our food have in explaining where we live, what we look like, and how we behave?  I study how properties of prey – material, structural, and ecological – shape the evolution of predators.  Specifically, I am interested in how animals adapt to novel foods and diets that pose unique challenges: prey that are tough, stiff, hard, or just generally robust.  I approach these questions at the macroevolutionary (how species are related) level; biodiversity lends insight into engineering and synthetic design based on an understanding of how animals evolve using similar organic principles.

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Help crowdfund shark research: Quick(silver?) stingrays

marine science, Natural Science, ScienceJune 10, 2016

KadyKady Lyons is a Ph.D. candidate whose research focuses on the intersection of physiology, ecology and toxicology.  Her Master’s at Cal State Long Beach with Dr. Chris Lowe got her involved in elasmobranch toxicology.  She is interested in how elasmobranchs respond to anthropogenic contaminants and how contaminants can be used as another tool to study ecology.  Currently, her Ph.D. is examining how accumulation of these man-made contaminants influences round stingray growth and reproduction. As part of her Master’s work, she began to investigate mercury accumulation and body distribution of mercury, a potent neurotoxin, in elasmobranchs using the round stingray as a model species. She is continuing to work on this project and will be raising funds to finish this research as part of The Experiment’s Sharks Grant Challenge beginning June 8th and running through the Discovery Channel’s Shark Week.

Mercury concentrations in the earth’s atmosphere have significantly increased with human activities such as mining and fossil fuel burning.  Mercury can be transformed into its more dangerous form (methylmercury) and this form is what becomes concentrated in animals’ tissues.  For animals that occupy higher positions in the food web such as elasmobranchs (sharks, skates and rays), mercury can bioaccumulate to high levels due to their long life and carnivorous behavior.

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Staff: Andrew David Thaler (1095), David Shiffman (493), Amy Freitag (235), Guest Writer (75), Chris Parsons (49), Kersey Sturdivant (47), Chuck Bangley (18), Michelle Jewell (16), Administrator (2), Sarah Keartes (1), David Lang (1), Iris (1), Michael Bok (0), Solomon David (0), Lyndell M. Bade (0)
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