Wading Through Research

Guest Post from Alex Perez, undergraduate researcher in the Seagrass Ecosystems and Marine Macroalgae labs at FIU. --------------------------------------------------------------------------------------------------------------------------------- When one thinks of Florida Bay the connotation is that of a shallow water system that is surrounded mangrove tree islands and mud banks. The thoughts of aquatic vegetation and blue water coloration more diverse than your standard 8-pack Crayola box, is what I used to think of. That is of course before I began to notice what was soaring above the surface. My first taste of the birds of Florida Bay was an experience I have yet to repeat, one chilly winter day as we were making our run from the western portion of the Bay to the center of the Bay we came across thousands (not a hyperbole) of migratory birds. The sound of our outboard shattering the tranquil water exciting the birds to take flight, was the first time I really no...

"Nothing endures but change." -- Heraclitus It is indeed a time of change for the FCE LTER graduate students. One of our own, Ann Hijuelos, Trexler lab master's student and blog founder, successfully defended her thesis and has moved on to greener pastures (a real job in Baton Rouge, LA). On behalf of all of us here at the blog, I thank Ann for her leadership and wish her well in all future endeavors. In the power vacuum that resulted from Ann's departure, Jenn Sweatman, Fourqurean lab PhD student, has forcefully taken the reins of the blog and we can only hope that she is a kind and benevolent master. I am very confident that Jenn will lead us to new heights of blogitude! Also, thanks to the fearless leadership of Dr. Evelyn Gaiser and the hard work of many other FCE contributors, our NSF grant has been renewed for another six years in the amount of $5.88 million! This grant renewal ensures that vital FCE research will continue until at least 2018, and a new crop o...

As I sit here struggling to write my very last blog post, I wonder "What can I leave people that they'll find useful in any way?"  I could provide meaningful insight on what it was like being a graduate student in my lab, but my thesis sucked all the meaning out of my brain and suddenly I can't even manage to put two sentences together that make sense.  So instead, the most useful thing(s) I can leave you all, is (are) my bookmarks!  Those that know me know how incredibly organized (read: obsessive compulsive) I am, so over the last 2.5 years I've collected quite a bit of useful internet knowledge and organized it into various categories on my computer.   So, as my parting gift to you, I leave you these helpful links on everything from job sites, to SAS codes, to data portals, and most importantly, sites for procrastination.  I can't promise these links will stay active forever, but last I checked they worked.  So enjoy!

Do you see the tiny green film at the bottom of the beaker in the picture above?  This extremely small clump of green stuff is a diatom sample weighing less than 20 milligrams that I need to carefully process and guard with my life for carbon isotope analysis. If I lose any of this sample or ruin a procedure, I will likely have to spend several weeks waiting for a new culture to grow and start over again.

This guest post was written by Deanna Conners, an environmental scientist and freelance science writer who holds a MS in Environmental Studies and a PhD in Environmental Toxicology. Deanna is a frequent contributor to  EarthSky . You can follow Deanna on  Twitter   and  Google+ . ------------------------------------------------------------------------------------------------------------------------- Image courtesy of Dwayne Bent via  Flickr  I’ve heard many people say that they enjoy science blogging. I agree, it’s fun. I’ve been blogging now for almost two years, mostly about topics in Earth science, and the science I write about never ceases to amaze me. I’ve never heard any scientist say that they enjoy writing journal articles. For myself, and I imagine for a few others, the joy associated with writing journal articles comes not from the act of writing per se but from seeing good research get published in good journals. The act o...

I'm just going to go ahead and say it: graduate school is great (though  The Simpsons disagree ). We're given 2-9 years (depending on whether you're a masters or doctoral student and the scope of your research) to live in a cozy academic bubble surrounded by like-minded peers doing research on things we think are interesting and important. We teach, we write, we think, we analyze, and we get to explore new places and meet really smart people. We don't have tons of extra responsibilities like kids (usually) and onerous administrative crap, and we're given some room to fail every once in a while (the most important part of the scientific process). Sure graduate school can be frustrating, annoying, and just plain idiotic at times, but that's pretty much a definition for life. Let's not get bogged down in the mundane. But the question I've been asking myself recently is, what's next?

I would like to introduce you to a new rising star in the FCE, Sara Osorio! She has been working with FCE LTER Education and Outreach coordinator, Mr. Nick Oehm, and our lead PI, Dr. Evelyn Gaiser. Her research project is about the diatoms found in the wetland restoration area of the Deering Estate ( Biscayne Coastal Wetlands Project ). Sara Osorio, FCE LTER High School Researcher at the FIU Periphyton Lab

During my first year as a graduate student, a week didn't go by where someone didn't ask me "So what's your research question?"  I hated that question more than anything.  I had combed the literature, searching for research ideas, only to discover everything I was interested in had already been done a hundred times over.  All of the mysteries of the environment had been answered and there wasn't anything left to be studied.  "Why am I even here and why are any of us doing science," I frequently asked myself.   "Ecology is stupid.  Ecology is hard.  I hate Ecology!" were also common chants I shouted in my office (and by office, I mean the spare lab next door that was used for storage and sleeping quarters for homeless grad students).  Then, one day, it suddenly all made sense.  I realized I was being punished by my adviser, because he was punished by his adviser, and his adviser's adviser punished him, etc. etc....

It is complex question, which merits thoughtful engagement with south Florida’s history, familiarity with ecosystem restoration theory and a good dose of visionary thinking. As scholars have demonstrated, ecological restoration is not just a scientific endeavor. Ecological restoration is also a social and political process that poses tough philosophical questions about what people’s proper relationship to nature should be (1). Yet, this question becomes all the more important in the current era of unprecedented environmental change.

The Everglades is our backyard, and that backyard is HUGE!   Fourteen cities of Miami fit in the Everglades. But in exchange for the high-rises, freeways, and spanish-tiled roofs there are tree islands, sloughways, water, pines, mangroves, birds, alligators, fish, spiders, mosquitoes, and plenty of beautiful scenery. The vastness of the Everglades provides prodigious niches of scientific interest to pursue. Some of us study the impacts of the drainage and canal system that line the perimeter or pierce through the Everglades. Other scientists scrutinize the causes of vegetation community structure changes. Some research predator/ prey relationships and others, the animal movement between biomes. Some study the water cycle and the physical and chemical interactions between surface water and groundwater*.   But before we can crunch all the numbers, write all the papers, graduate and go off to save the world, we need to take the measurements, collect the samples, ...

Guest post today from a new member of the FCE community! -------------------------------------------------------------------------------------------------------------------------- Howdy ya’ll! I’m one of the newest members of the  Trexler lab , here all the way from Houston, Texas. I finished my Masters in May, which focused on reproductive life histories of small stream fishes. In addition to working in some amazing clear water East Texas streams, I have a love/hate relationship with springs in the beautiful West Texas Chihuahuan desert. But, life hasn’t all been unicorns and butterflies; I’ve worked in my share of dumpy freshwater sites. However, nothing prepared me for what I was to endure in the Everglades. 

I've always had a passion for animals, particularly large animals of the dangerous variety (big predators), but before I started my PhD I had never really spent much time thinking about alligators. Now, after working with alligators in the coastal Everglades for the past 5 years, they are one of my favorite animals. Let me tell you a few reasons why:

My research is on the diatom communities of the Everglades. These silicious, environmentally sensitive algae like to live buried within a complex biofilm called periphyton .With the naked eye, periphyton just looks like muck or scum. But there is a hidden microscopic world that is quite fascinating and even beautiful. Everglades periphyton magnified 1000x: filamentous cyanobacteria and a diatom

Whether we are working in the field or in the lab, the things we have to wear to do our work make us stand out from the undergrad crowd at our universities. Below, I have listed the latest styles for Fall 2012 Everglades research:   Field Tannin-dyed Pants   Above is a picture of pants that I wear in the field. These pants are naturally tie-dyed with streaks of grey and orange from various organic compounds floating around in the water. The key rule in Everglades fashion is to never wear anything nice or new, so these khaki pants that I’ve had since 9th grade are perfect for the field.

Good morning everyone, This blog is a tribute to all the animals that get caught up in science. Without their help, we would know alot less about the environment and the natural resources we all love! Lobster toupee None of the other lobsters can tell its scientific equipment: These tags are the same as the ones I use . They send a sound pulse that can be detected by underwater equipment and are used to track movement patterns (photo courtesy of FWRI http://myfwc.com/research/saltwater/telemetry/) Gopro shark (insert dup-step music here)   These are cameras attached to the sharks back that used to video and understand shark feeding habits. Courtesy of the Shark bay ecosystem research project and the Heithaus lab (http://www2.fiu.edu/~heithaus/SBERP/projects/tigerres.html). Punk rocker walleye… His girlfriend’s parents are not impressed   Lip tags are used in mark rec...

For Long-Term Ecological Research (LTER) research in the Seagrass Ecosystems Lab, we venture out into Florida Bay every two months to do a survey of the submerged aquatic vegetation (seagrasses and macroalgae).   As I mentioned in my last post ( Florida Bay:  Beneath the Surface ) Florida Bay is a honeycomb of basins, which creates different habitat types.   These different habitats, specifically the type and density of vegetation on the floor and sediment type (and many other factors that are beyond the scope of this post), attribute to the color of the water.   In a single LTER trip, we see water ranging from deep blue to teal, green, and even brown!    After 2 years of running the LTER project for our lab, I am still amazed by the dynamic nature of Florida Bay on the surface and below.

Our full time bloggers are recovering from the  FCE-LTER Beach BBQ  this weekend so we've asked Mike Bush from the Department of Biology to talk about his research on fish movement in the Everglades. --------------------------------------------------------------------------------------------------------------------------------------- Identifying patterns of animal movement is an important part of most conservation programs. As Everglades restoration continues, identifying how fishes respond to changes in water flow, removal of levees, etc. will provide us with important information about how restoration is changing the Everglades. I’m going to briefly discuss some of my work with large fish movement in the central Everglades.

In continuation of Ann’s post a couple weeks back, conferences and meetings are very important in becoming a successful and knowledgeable graduate student. Currently, I am in Estes Park, Colorado, which is about 1.5 hours outside Denver and adjacent to Rocky Mountain National Park for the  Long-Term Ecological Research All-Scientists Meeting . In a nut-shell, this meeting is held once every three years and brings together scientists and researchers from 26 LTER sites around the country and around the world. This meeting differs from a conference by being primarily focused on cross-site and interdisciplinary collaboration. This is done by holding working group discussion sessions surrounding a particular topic. Scientist that are interested in that topic can participate in a discussion session that has a specific outcome; typically information exchange, brainstorming, or a product such as data analysis or a journal article.  

Our regular bloggers are out gathering data so today we have a guest blogger, Stephanie Long from the Department of Earth and Environment .  ---------------------------------------------------------------------------------------------------------------------------------------- Despite all of the extreme weather reporting and constant television coverage, Hurricane Isaac was just another storm for most of South Floridians. The only trouble the storm brought us was copious amounts of rain. So when I got a chance to go take samples along the L30 Levee just three days after the storm had passed, I was given a very fundamental lesson in South Florida hydrogeology.

One of the great joys of science, in my view, is teaching others about science, how it works, and why it is arguably the most advanced type of problem solving ever invented by humans. As graduate students at FIU we are given ample opportunities to pass along our knowledge, expertise, and love of science to the next generation of scientists (undergraduates) through teaching classes, giving public lectures, and directly mentoring individual students. At last count FIU had about 40,000 undergraduates enrolled, so finding motivated students to help out with graduate research is a relatively easy task.

Greetings from St. Paul, Minnesota!  I have left the sweltering heat of south Florida for a few days to attend the American Fisheries Society Conference .  Attending conferences is a must-do for graduate students.  It's a chance to share your research with a large, scientific audience, get feedback from the top scientists in your field, and make connections (and new friends) along the way.  These meetings can be a bit overwhelming so I've generated some tips to help you get through them:

Good afternoon everyone! I hope everyone had a good summer! For us, school is beginning, once again FIU has become a large traffic jam.  And as I was sitting in my car waiting to leave FIU, I came up with this blog idea. When is accomplishing nothing, more than just accomplishing nothing? 

Greetings from the confines of my office!  I have not posted in over a month but lucky for you, the other bloggers have kept you entertained with Alligator vomit , post-quals stress disorder and the joys of working with carcinogens, flammable materials and high-voltage equipment .  If those don't make you want to be a graduate student and/or scientist, then I don't know what will! So what have I been doing?  A whole lot of non-exciting blogging material like processing DIDSON videos , analyzing data, and preparing for conferences.  The good news is now I have some results to share!  

Today’s post is the last installment of my series “Grad Student Life Beyond Fieldwork.” Take a look at Part 1 (Classes), Part 2 (Teaching) and Part 3 (Our Offices) to read about other facets of grad student life. Part 4, the post you are reading now, is about the labs where we produce and analyze data.

The first half of this year was a pretty tough time for me. I was preparing to take my qualifying/comprehensive exams, also known as 'Quals'. For the FIU PhD student, these are the exams you must pass in order to become a PhD candidate, which is the point you prove your worthiness/ability to finish and get the okay to continue with your graduate program. At FIU's Biology department, the exams usually consist of 1 day of written responses to questions from each of your committee members (that means 5 straight days of writing) and, about 2 weeks later, a 2-3 hour oral exam with your whole committee. The format can vary based on committee members' preferences or department rules. You receive the official title of PhD candidate once you defend your dissertation proposal, after the exams are over.

Florida Bay consists of mud banks so intertwined it takes an experienced boater (or a great GPS chart tracker, if you’re me) to successfully navigate across the bay.   Because flow is somewhat restricted by these mud banks, the basins have developed into unique habitats making each dive of the FCE-LTER seagrass sampling project quite different.   At each of the LTER sites within Florida Bay, we estimate percent cover of all seagrass species and many calcareous green algal species, as well as red, brown, and other green algae.   We monitor water quality over time via nutrient analyses in seagrass and calcareous green algal tissue, and we collect data on salinity, temperature, light penetration, and water turbidity.   Data are located at www.fiu.edu/~seagrass .

Ever wonder what an alligator's breath smells like? One of the perks of my research is I get to hang out within sneezing distance of the amazing reptiles and I can tell you from first hand experience that their breath smells like death. Two of the major questions I try to answer with my research is what do alligators eat in the coastal Everglades and where do they eat it? To get at these questions, I use two different techniques: stomach contents analysis (SCA) and stable isotope analysis (SIA).

When one thinks of a student doing research in the Everglades, one would assume that the researcher is an outdoorsy type who could never thrive in an office or indoor work environment. Part 3 of this series, however, is about grad student offices, which is where some of us actually spend the majority of our time. If you haven't been keeping up with this series, you can learn more about the other aspects of grad student life in Part 1 and Part 2 of "Grad Student Life Beyond Fieldwork."

The limousine pulls up to the opera house... The patrons step out wearing their summer fashion...

What data organization looks like (aka what I've been staring at all day today):

It is more than likely that you have already encountered periphyton of some form. You may have encountered it without even really noticing it or knowing what it was. Or you may have thought it was pretty gross. Periphyton is a bunch of algae, fungi, other microbes, and dead material either growing or aggregating together on or around a surface. “Peri” means around (like in perimeter) and “phyto” means plant. The plant part refers to the algae that are a major component of periphyton. Periphyton can grow on plants (epiphytic), on rocks (epilithic), on top of the sediment surface underwater (benthic), and even on animals (epizooic). Periphyton has been called “pond scum,” “muck,” or even “rock snot.”

What do FCE grad students do besides trekking through mangroves, collecting water samples and battling mosquitoes? My four part series, “Grad Student Life Beyond Fieldwork,” is designed to give readers of this blog a general idea of what we do when we’re not in the Everglades. Whether you’re a prospective student wanting to know more about grad school life or a PI wondering why we haven’t finished analyzing our data yet, we hope this series gives you a more complete picture of what we do. Part 1 covered graduate coursework and degree requirements. Today’s post, Part 2, covers our experiences as teaching assistants.

To study American alligators that live in the coastal Everglades you need to be a bit of a night owl. Alligators are much easier to find and catch at night because their eyes glow bright red when you shine a spotlight at them, whereas during the day they blend in amazingly well with the water and the vegetation because of the sleek, low profile of their bodies.  Fortunately for me, my natural sleep patterns involve staying up late and waking up around noon.

For those of you who read Using "Sound" to See Underwater  and Everglades at Night ,  you've learned a bit about the DIDSON (an imaging sonar) and have gathered that some of my work occurs at night in the glades.  Below, I'll explain how I'm using the DIDSON to understand the role of predatory fish in canals of the Everglades.

Dwarf Bald Cypress Trees and an Expansive Sky in Big Cypress National Preserve Photo courtesy of author What does an iconic place like the Everglades mean to people, and how does this shape their perspectives on how it should be stewarded? This is one of the questions I explore in my dissertation research on the Big Cypress National Preserve in the southern Everglades. My work documents the contemporary debates and discussions between environmentalists, the government and local people about how this stunning natural and cultural landscape of cypress strands and freshwater sloughs should be managed and protected. As part of my research, I examine how these groups’ different perspectives are tied to the ways they uniquely know the Everglades.