The decline and fall of the literature review

Academic life, publishing, Science publishingMay 16, 20160

I’m currently doing an annual review of environmental impacts on whales and dolphins for the International Whaling Commission, which involves assessing, reading and potentially summarizing almost everything that’s published on cetacean conservation. Every year this exercise gives me an ulcer because: (a) climate change and pollution threats are accelerating; (b) reiterated recommendations from scientists from many, many previous years have yet again gone unheeded; and (c) some endangered species get closer and closer to extinction, yet most of the funding goes to research questions whose answers we really already know rather than to practical conservation. It’s all rather depressing …

end-is-near

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A precautionary approach to health, safety, and conservation while 3D printing in the home.

Conservation, Education, EnvironmentalismMay 13, 20160

3D printers are awesome.

A Printrbot in the home.

A Printrbot in the home.

That sentiment really shouldn’t surprise anyone who follows this blog. From oceanographic equipment, to farm tools, to just things around the house, over the last year I’ve made 3D printing a standard part of my toolbox.

A conversation last week on Twitter got me thinking again about 3D printers, safety, and disposability. On one hand, by allowing us to fabricate intricate custom parts at home, 3D printers can help us reduce the amount of waste produced and allow us to extend the life of otherwise disposable items. On the other hand, 3D printers produce their own plastic waste, particularly if, like, me, you develop a lot of new projects from scratch.

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Six thoughts about Greenpeace’s attack on Ray Hilborn.

Conservation, policy, Science

First, some background:

Or, just read Trevor Branch’s timeline.

1. The idea that scientists should declare every source of funding over the history of their career on every scientific paper is impractical and wholly unnecessary in a connected world where anyone can effortlessly access a researcher’s CV. Non-profit NGOs only need to file one financial disclosure statement every year, not attach it to every press release, and that is also perfectly adequate.

2. Transparency in funding is important. Claiming that a researcher is failing to disclose funding information when that information clearly is available and accessible erodes public trust in science and makes everyone’s job harder. Greenpeace didn’t send a team of stealth lawyers on an o’dark thirty raid of the UW mainframe, they asked for the information and were given it.

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Build your own BeagleBox 2!

Life in the LabMay 9, 20160

A more comprehensive build guide, along with the 3D printer files, can be found in the BeagleBox GitHub Repository. 

 

The BeagleBox 2 is a dirt-cheat, tough, versatile field computer built from 3D-printed parts, off-the-shelf hardware, and a single board computer. You can read all about it here: The BeagleBox 2: a dirt-cheap, tough-as-nails, 3D-printed, versatile field laptop.

Let’s build one!

The Brain of the BeagleBox 2

The Brain of the BeagleBox 2

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Introducing Field School: A Resource for Marine Science Research and Education

Citizen Science, Conservation, Education, fisheries, marine science, Natural Science, Science, sharks0

julia_staffJulia Wester  is the Director of Program Development for Field School. She received her PhD from the Abess Center for Ecosystem Science and Policy at the University of Miami in 2016. Her dissertation studied the psychology of decision making about the environment, specifically with regard to limited water resources. She also received a Msc with Distinction in Biodiversity Conservation and Management from Oxford University and worked as a Legislative Aide in South Florida, focusing on environmental policy. She has consulted with nonprofit programs to evaluate their educational programs and assisted with training staff to conduct effective public outreach.

Field School logoThe folks at Southern Fried Science, as part of their commitment to research and education, have generously given us this platform to talk about our educational start-up, Field School. (Thanks, SFS!). They’ve also been kind enough to get excited about working with us to develop and test new research techniques, study awesome animals and ecosystems, and improve marine science field education—so stay tuned for some of those upcoming collaborations!

What is field school? 

Field School is a hybrid company on a mission to support field research in marine and environmental science, and create high-quality educational and training opportunities for students and the public. We offer hands-on, research focused courses on a variety of topics, from corals to sharks, on our 55’ custom live-aboard research vessel.

Field School offers researchers and students opportunities to engage with and study tropical marine ecosystems. Photo credit: Kristine Stump

Field School offers researchers and students opportunities to engage with and study tropical marine ecosystems. Photo credit: Kristine Stump

Part of what makes Field School special is the team we’ve brought together. Our captain and crew all have doctoral and/or masters degrees in marine or environmental science, have authored numerous scientific publications, and have a combined 25 years of experience in field education and outreach. We have developed short- and long-term training and mentoring opportunities for students, teach highly reviewed and award-winning university courses, and work with partner non-profits to create outreach programs for the public. We collaborate closely with our scientific advisory board and partner universities to develop the conservation and research projects our students work on, ensuring their time in our courses is professionally relevant and meaningful.

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The BeagleBox 2: a dirt-cheap, tough-as-nails, 3D-printed, versatile field laptop.

Life in the Lab, Science0

The BeagleBox 2

The BeagleBox 2

Last year, as part of Oceanography for Everyone, we debuted the BeagleBox, a small, cheap, tough, basic field computer powered by a BeagleBone Black. The first BeagleBox didn’t promise much, it was designed for basic field work and, most importantly, to be cheap enough that researchers (particularly grad students) wouldn’t be too worried about damaging it. It wasn’t designed to be your only computer but to replace your more valuable computer when participating in fieldwork.

In the last year, the single board computer landscape has changed, with new systems running off tiny, powerful 64bit ARM chips. One of the first of this new breed of SCB to hit the market was the massively Kickstarted, and rocky-launching Pine64. I received my 1GB Pine64 late last week, and immediately set to work redesigning the BeagleBox to house this larger board (and correct for some other annoyances in the original design). So here it is, an even beefier, cheaper, tougher field machine.

Yes, it will run an OpenROV. It will not run it well.

Yes, it will run an OpenROV. It will not run it well.

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Learn what whale harassment looks like (GIFs)

Animal welfareMay 6, 20160

It’s nearly summer, which means the shores will soon be filled with SUP boards, drones, and self-professed whale whisperers.  This authentic lifestyle is an obnoxious time for marine mammals, and soon your online feeds will be flooded with aerial footage of people “sharing the water” with marine megafauna.  Some of these shots are innocent but an increasing amount are harassment.  Below is a helpful GIF guide to tell the difference.

Not harassment:

not whale harassment

Also not harassment:

not whale harassment

These scenarios happen.  They are rarely documented and totally amazing.

not whale harassment

(c) Dave de Beer, Cape Town

The below GIF explains what whale harassment looks like:

whale harassment

It’s truly that simple.  The next time an amazing 4K aerial shot shows people interacting with whales, ask yourself two things:  1) Is the whale’s head or the tail facing the people?  2) Are the people actively approaching the whale?

If the answers are 1) Tail and 2) Yes, that is harassment.

Remember:  Whales, dolphins, sharks, or anything else in the ocean does not have to interact with you, even if you brought your drone and your Instagram feed is a bit lacking.  It is illegal to harass marine mammals because it is potentially life threatening for both you and them.

Big ideas and little robots: Using the OpenROV in interdisciplinary STEM projects

A Renewed Sense of Wonder, Citizen Science, Conservation, Education, Natural Science, ScienceMay 4, 20161

portrait-joeyJoey Maier is a biology professor at Polk State College where he uses every possible opportunity to encourage his students to spend time in the water, play with technology, and do #CitizenScience. As an undergraduate, he did a stint as an intern for Mark Xitco and John Gory during their dolphin language experiments.  He then spent the years of his M.Sc. at the University of Oklahoma thawing out and playing with bits of decaying dolphin.  After discovering that computers lack that rotten-blubber smell, Joey became a UNIX sysadmin and later a CISSP security analyst.  

While his pirate game is weak, he is often seen with a miniature macaw on his shoulder. His spare time is spent SCUBA diving and trying to hang out with people who have submersibles.  You can follow him on Twitter or Facebook.


There’s a Klingon bird of prey hanging from the ceiling in my office.

I may teach biology, but at heart I’m a sci-fi nerd.  Naturally, I’m interested in futurism, robots, lasers and all manner of techy paraphernalia.  I’d been watching the OpenROV project for a while, but hadn’t gotten one yet.  They were obviously awesome little machines that gave me a serious case of gadget envy, and I knew that some of our students would love to pilot an ROV.  I needed a much better reason than that, however, to justify getting one.  There’s no line item in our budget for, “Wow, that’s cool!” and I was fairly certain that the college administration would tend to favor lower cost and more familiar forms of student engagement

Photo courtesy Joey Maier.

Photo courtesy Joey Maier.

This tweet changed everything.  When I found out that Andrew had designed a mini-Niskin bottle, the wheels in my head started turning.  Assembling an OpenROV would, naturally, be a very STEM-oriented project.  The times our students piloted the ROV could become water sampling field trips, and the kids could analyze their samples back at school as a laboratory activity. If students recorded the process, they could make a short film. I mulled over the possibilities and bounced ideas off of my dive buddies during the hours we spent traveling to and from the coast. (more…)

The tuna that ate a seagull, and other bird swallowing marine megafauna

biology, ecology, marine science, Natural Science, sharks, UncategorizedApril 26, 20162

Seagull swallowed by tuna

Once again, the internet is in a fervour over a rarely documented, but pretty common, animal interaction.  The video below shows fishermen at a pier in L’Escala, Spain tossing small fish to a tuna.  A nearby seagull went for the same fish and was ingested by the tuna, much to everyone’s surprise.  Naturally, the tuna spat out the seagull, luckily uninjured, and it flew away to dive another day:

Seabirds are often ingested by marine megafauna since both groups forage in the same areas, often on the exact same prey.  This video was an artificial overlap of foraging animals created by the people tossing fish from the pier, but in natural settings where two animals feed on the same prey and one of those animals is considerably larger than the other, the smaller animal faces a pretty high risk of being swallowed.

This is especially true for lunge-feeding whales that take in large mouthfuls of fish, water, and anything else at the surface.  Haynes et al. identified three Glaucous-winged gulls in the fecal remains of foraging humpback whales in Glacier Bay, Alaska.  The birds were mostly intact, suggesting that humpback whales aren’t capable of digesting birds well (we’ve all been there).

All of the examples above are accidental ingestion, but some marine animals deliberately target birds for food, too.  Tiger sharks seasonally aggregate at the Hawaiian Islands of French Frigate Shoals to forage on albatross fledglings.  Fledglings are fat, slow, and naïve, making them easy and profitable prey.  This foraging strategy is common among sharks and is the same reason white sharks target seal colonies during South African winters.

The alien giant catfish of the river Tarn in southwestern France is an aquatic example.  They have also acquired a taste for feathered food and learned to ambush aloof pigeons, with a success rate of 28%:

Although not mega- megafauna, the Hilaire’s Side-necked turtles of Brazil have been documented consuming pigeons in a scene that honestly rivals Jaws.  Who’s slow now? (Edit: Thanks to @mattkeevil for the reference!)

Marine and aquatic animals do indeed eat birds, accidentally and deliberately.  Exactly how regularly this happens is unknown, but this antipodean pairing is essentially the chocolate shake and fries of the natural world.  The bottom line is, if you are in the same space where something bigger than you is foraging, you might get swallowed.  Birds, and humans, alike:

The Science of Aquaman: Understanding Dead Water

Aquaman, Natural Science, oceanography, Popular Culture, ScienceApril 22, 2016

Update: legendary oceanographer Dr. Kim Martini stops by to set the record straight on the challenging subject of internal waves. Her comments in bold. 

It has been a long time since I’ve made an entry into our long-running, world-famous, Science of Aquaman series. The last few runs have been heavy on high adventure, but light on ocean tidbits for me to nerd out on. I don’t like to force ocean fact into comic fiction unless the opportunity presents itself.

So, with the newest run of Aquaman, starting with issue #50, focusing around a villain named Dead Water, I thought it was the perfect moment to talk about some physical oceanography. And then…

Dead Water. From Aquaman #51.

Dead Water. From Aquaman #51.

My hat’s off to Dan Abnett, who beat me to the science punchline. If I had to explain the phenomenon of dead water in a single tweet, it would have been pretty close to this. Well played, sir. Well played.

So what is dead water and why does it make maneuvering a vessel so challenging?

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