The Science PhD Experience: My Life is a Series of Home Improvement Stores

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Source: Wikimedia Commons

Never when I signed up for this whole PhD “thing”, did I think that further down along the line I would wander down the aisles of countless formless and faceless Home Depots and Lowes, familiarizing myself with PVC epoxies, pipe cutters, types of quick-pour concrete, and erratically color-coded lengths of rebar. While I am in the very last throes of the natural science component of my dissertation, for stretches within the last year, nary a week would pass without at least one, if not several, trips searching for the miscellanea one needs to make a bare-bones scientific project happen.

My method for estimating oyster filtration rates required the use of sediment traps (see my post about it here) constructed out of buckets and netting. However, the studies that used them prior and upon which I based my design, had employed them in very different settings. My traps had to withstand dynamic ocean conditions, tidal cycles, and the interest of the errant passerby. So thus began the nail-biting process of iterative design. What type of buckets to use to avoid re-suspending sediment? What kind of netting across the mouth? How to affix them to reef? How to weight them so they wouldn’t float away during the first high tide?

Practice run after practice run unfolded as I tried various proto-types. Scuba weights affixed to the mouth of buckets using hose clamps. Testing ways to keep everything in one place using ground anchors, thin lengths of PVC, rebar. Phone calls from nearby good Samaritans who had retrieved my runaway equipment (a PSA if there ever was one for labeling your gear!). A slick (if not utterly lo-fi) double-nested bucket design weighted down with rounds of concrete emerged out the mixture of mishaps and successes.  I then did it all again and tapped into the same recurrent type of process when creating a seawater flow-through system for oyster filtration lab trials.

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All the while, I was running to every hardware store in town, looking for materials of the right shape, weight, and construction for whatever small application I had in mind. Many questions directed towards employees started with “This is going to sound strange, but…”. Eyebrows were raised when I bought 30 of something generally purchased in increments of one or two – “…Doing a lot of yard work this weekend?”  I recall poorly relaying the idea of my experimental sediment traps meant to measure the amount of oyster biodeposits produced during my experiment, and the amusing follow-up question: “Are you trying to keep the oysters from getting away?”

Many questions directed towards employees started with “This is going to sound strange, but…”.

Additionally I had the help of a marine lab machine shop to drill, cut, and sand. I learned how to estimate which equipment I needed for which job. I also had the opportunity to watch those inclined towards clever design and ask plenty of questions. Is there enough water pressure to do that? How do I get the flow to be more laminar? How do I keep this from leaking?

It’s a cultivated skill set, one which rewards those who tinkered with lego and kinex as a kid. Rarely are we told as marine biologists, fisheries scientists, or field ecologists, that we will draw so heavily upon what amounts to being back-of-the-envelope engineers.It’s also a continued argument for the inclusion of the “T” (technology) and the “E” (engineering) part of STEM training that is often desired on the job, but may make scant appearance in a scientist’s formal education.

Most of us instead gain experience through more informal avenues, as the best teacher is often necessity. Also there is no better practice than to constantly build, err, and deconstruct, all while slowly incorporating new fixes and experiencing the fog of confusion out of which comes little sparks of revelation. The act of literally building our science from the ground up is one of ultimate creativity, funneling in threads of right-brain function, and helping us shape solutions in response to whatever demands our research may make of us.

Note: This content has been cross-posted on the blog “From Reef to Rivers: Florida’s Fisheries Science Blog

Speck of Science – 4/19/16 – March of the Crabs

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Source: Animal Planet

Mass migrations fascinate me – massive swarms of creatures on robotic treks to satisfy deep-seated needs for resources – nature’s automatons reaching for food, for mates, for brighter skies. One of the earliest that captured my attention is expressed in this Animal Planet video documenting the movement of red crabs on Christmas Island:

http://www.animalplanet.com/tv-shows/wild-kingdom/videos/christmas-island-red-crabs/

(Note at 1:40, crustaceans seem to be playing “frogger” while obliviously scuttling across roads and railroad tracks. Not the unexpected result of the clash between crab and human.)

A gif of the oceanic equivalent has made a recent appearance online, showing an endless carpet of sandy colored scuttlers (they were in fact red,  or “tuna,” crabs who appeared that way as they stirred up a the sediment on the sea floor). However, this article sheds more light on the unusual event captured by a manned submersible exploring Hannibal Bank off of Panama (fitting name for the location of a slightly unnerving and intriguing event to occur? ). The following video comes from Woods Hole Oceanographic Institut and features scientist Jesús Pineda explaining the details around recording the migration:

 

 

Speck of Science – 4/6/2016 – Gimme Back My Buoy

I have been through a blogging dry spell lately, but nothing like starting out again with the amusing news of 2 men essentially holding a USGS (United States Geological Survey) scientific buoy hostage.

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A Map of the Monterey Bay Aquarium Research Institute’s Coordinated Canyon Experiment. The buoy was associated with this particular project. Source: MBARI

The buoy, which was deployed to gather data related to El Niño events, drifted off its mooring during a recent storm. Two fishermen chanced upon it, recovered it, and are now demanding $13,000 in exchange for its return. Their lawyer, a seemingly rather colorful character and self-described “old trial dog”, initially set the price a bit higher based on the following mathematics: ” On good days fishing they gross $2,700. Taking the big and gouging thing onto the boat and having it there kept the boat out of action for nine days for a multiply of $24,300. Twenty percent of value would be $80,000. We offer to SELL (you can use any other word you like in an agreement) it to you for $45,000.” One has to wonder why they took it upon themselves to keep the “big and gouging thing” on their boat for nine days in the first place.

The article notes from several sources that salvage laws likely do not apply here, especially as the buoy was never properly abandoned. However, the loss of and tampering with of expensive research equipment has always been a known and pervasive issue in oceanic research.  I for one will be interested to follow the outcome of this eyebrow-raising case.

Depth of Field #2: The Sea Hare Emerges

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Photo Credit: Carrie Schuman

The sun is starting to set on expanses of mirror-reflective tide pools speckling the beach of the Tawharanui Marine Reserve in New Zealand. I’ve been walking along staring into them at random in my search for anything novel when I chance across what is at best guess an example of Aplysia dactylomelathe variable sea or spotted hare.

In a surprising contrast to the small chitins, tunicates, and other finds, the sea hare was relatively large, measuring somewhere in the range of 5 to 6 inches in length. As seen in this additional photo, a smattering of spots can be seen along its body:

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Photo Credit: Carrie Schuman

According to this source, sea hares are hermaphroditic though they do not practice self-fertilization. They may often form reproductive “chains”.

As suggested by one of their common names, they may be highly variable in appearance with their coloration primarily determined by the type of algae they feed on.

They release a purple dye as a mechanism to surprise and confuse predators. This particular characteristic was one I had once experienced first hand when handling my first sea hare in the mangroves of Key West. It certainly has a startling quality to it.

Variable sea hares tend to be more solitary, and nocturnal in nature. So perhaps no small amount of dumb luck governed this thrilling little chance encounter.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Aplysia dactylomela

Speck of Science – 1/7/2016: Aye Calypso

Sometimes I come across some interesting news item that I don’t have time to write about in depth but still want to share. I’ve decided to start a new Speck of Science feature on my blog as a way to share brief blips and recaps of internet curiosities and dispatches.

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Today’s item is an article from the Guardian reporting that Jacques Cousteau’s ship, the Calypso, will soon be ready to begin life anew. The ship was downed by an accident and since 2007 had been languishing in a sort of boatyard purgatory due to disagreements over payment and the purpose of its restoration. This is truly exciting news for the continuing legacy of marine exploration, and our care for the world’s oceans.

 

 

 

 

 

Depth of Field #1: Coquina and the Palm Coast

“Photography is the only language that can be understood anywhere in the world” – Bruno Barbey

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So I’m one of those people who use facebook as an image repository – a sort of dusty social media shelf where I can look back and browse through digital photo albums filled with virtual Polaroids (I grieve the fact I never owned a Polaroid camera). However I recognize that the often interesting stories related to these images are buried relatively quickly.

This is the first entry into what I plan on making a regular feature (perhaps weakly-ish?). I will unearth what will generally be a nature or ecology-centric photo and jot down a few words about the context in which the photo was taken. If nothing else, I think this develops some nuance to my interest in cultivating a presence as a science communicator.

The first photo I’m featuring is taken very near where I work on my dissertation research. The shoreline is from Washington Oaks State Park in Palm Coast, Florida – a half hour or so south of St. Augustine. This was winter in Florida which is still punctuated by the vibrant green of algea growing on coquina rocks.

Coquina is a very marine phenomenon – the sedimentary rock consists primarily of Donax variabilis shell – the tiny little Coquina clam. Shells originating from other molluscs and invertebrates may join the mix. The rock was used for many of the Spanish Colonial structures – primarily forts – in the St. Augustine area.

One of the most notable and striking features of the Coquina are the circular depressions weathered through the rock. The shells that comprise the rock are largely composed of calcium, making Coquina a type of Limestone, which is relatively soft and easily shaped by the elements and other influences. A couple sources I’ve found suggest these holes are from Coquina forming around cabbage palms at one time. They certainly make for a visually arresting landscape.

 

 

 

 

 

The Little Things Add Up: Banning Microplastics in the U.S.

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Photo Credit: Kunnskap/Wikimedia Commons

According to a recent piece in The Guardian, a bill was approved by the House of Representatives that would phase out the use of microbeads in products used within the U.S.

While microbeads have use in scientific contexts, such as breaking open cells for DNA and RNA extraction, they have been pervasively appearing in cosmetics and general consumer products in more recent years:

Microbeads may have significant environmental impact, especially within aquatic systems, as these microplastics may be washed down the drain with regularity. In addition, other small micro plastic particles may be formed from the breakdown of larger plastics introduced into these same environments.

The small size of these particles may parallel that of small microscopic organisms and so may be accidentally ingested by zooplankton, or other creatures that filter feed. See the below video capturing a copepod capturing fluorescently labeled beads with the use of feeding currents:

In addition to then biomagnifying up the food chain into other organisms, these fragments have also been shown to both release and absorb pollutants.

So the recent legal action is certainly an exciting victory. See a timeline here of some of the actions that have been leading up the bill.

 

Whale Tales – Current Cetacean Communiqués

Orcas as captured by drone surveillance. Photo credit: NOAA, Vancouver Aquarium.

There’s been a couple interesting whale-centric stories I’ve come across lately, so I thought I would share on the blog.

While the idea of drone surveillance is proving to make a large part of the public uncomfortable, the technology is proving to have less pernicious applications in observing natural phenomena.

Southern resident orca calf nursing. Photo credit: NOAA Fisheries, Vancouver Aquarium.

With regards to whales, drone footage of southern resident orca pods has recently been captured by a collaborative effort between the Vancouver Aquarium and NOAA (National Oceanic and Atmospheric Administration).  NOAA recently released beautiful close-up photos and a video conversation with ecologist John Durban giving some additional context to the what the drone captured.

Over more recent years with advances in genetics and stronger observational data, it was determined that orcas are not a uniform species and instead vary with regards to morphological characteristics, ecology, and behavior, generally referred to as “ecotypes”. The southern resident population of killer whales numbers about 81 individuals. Aerial footage provides a relatively non-invasive way to study and collect data on these animals.

Read more about the study and about “mobly”, the hexacopter used to study these creatures, here.

Another fascinating footage find was this picture posted of an albino southern right whale calf off the coast of South Africa:

Anton Schutte was alerted to its presence by a tourist he had recently befriended and was able to snap pictures and video of the blindingly white baby whale.

Omura’s whale lunge feeding. Photo Credit: Cerchio et al 2015.

Lastly, Discover Magazine released an interesting news bit based on a recently published paper about the Omura’s whale. This whale wasn’t classified as its own species until 2003, and was described based off of samples from carcasses that had washed onto beaches. Scientists spotted living populations off of Madagascar and were able to genetically validate the sighting as Omura’s whales. Surveys were completed over a course of 7 years in order to learn about their ecology and behavior.  They have rorqual pleats like those seen in humpbacks, that allow them to “lunge feed” – quickly engulfing large masses of water and using their baleen to assist with filtering out their prey items. They sport an asymmetrical white patch on their lower jaw, much like Fin whales. They also likely do not wander far from their home base.

Hope you enjoyed the updates. Until next time my friends!