Tuesday, October 30, 2012

Hurricane Sandy visits Boston

I suppose I can now say that I have been through my first hurricane.  Growing up in the Midwest, hurricanes were something that I only heard about on the news.  I would watch videos of rain jacket clad weathermen struggling to stand upright, but I never really expected to see it firsthand.

Hurricane Sandy brought plenty of rain and wind to Boston yesterday, but for us the worst is past.  Yesterday Boston University closed both campuses and the MBTA stopped all mass transit service at 2PM.  My roommates and I stayed home and settled in for a day of matlab homework and studying, as the wind gradually picked up throughout the day.  By early afternoon we were watching people who had gone to work in the morning head home and struggle to stand upright in the wind.  As the day went on, the storm only continued to grow.  According to the National Weather Service, by evening we had reached peak wind gusts of 64mph in the area where I live.  We could see trees across the street swaying back and forth and rain pelted our windows.  This continued for several hours but eventually the winds began to die down and the storm quieted overnight.

Despite the hurricane yesterday, this morning Boston is already getting back to business as usual.  As I walked to work this morning I saw some branches down and leaves littered the streets, but the day feels more like a rainy spring day than the morning after a hurricane.  The MBTA has been running since 8AM and BU officially reopens at 11AM (though many grad students have been back to work for a couple hours already!).  Power is still out for thousands of people across the state but it is slowly being restored and much of the city is already up and running.  [In fact, most of the area where I live never lost power- even during the peak of the storm.]  All in all...Boston dodged the worst of it.

Sadly New York and New Jersey did not fare as well.  Our thoughts and prayers will be with them as they face a long cleanup process and try to put their lives back together.

PS- Science did not stop for the hurricane.  I worked on matlab from home but evidently one of my labmates ran the TIMS during the hurricane and the other was so focused on writing his dissertation he didn't notice that a tree fell in his front yard.  Ah grad student life.

Wednesday, October 24, 2012

TIMS Tutorial: The Basics

Monday morning I finished the first drafts of all three of my NSF graduate research fellowship application essays.  Monday afternoon\Tuesday morning I finished this week's homework set for the applied statistics course I'm taking.  But now it's Wednesday afternoon and today I feel like I haven't completed anything besides discovering new research roadblocks.  It seems like graduate school is full of bursts of fairly impressive productivity followed by lulls where the instrument doesn't work, experiments fail one after another, and the to-do list gets longer and longer but nothing gets marked off.  If anyone with vastly more science experience has tips for how to overcome lulls I'd be happy to listen!

In an attempt to do something productive and work on my science communication skills (I need all the practice I can get...qualifying/comprehensive exams are looming!) I have decided that one of the projects I'm finally going to tackle during my lab work lull is to write about the main instrument that I use in my research.  Plus, I often learn best by teaching!  I've been meaning to do this for a while and if you've seen references in my posts to "the instrument" or "the TIMS" and wondered what on Earth that was..this is the series for you!  Hopefully, today's post will provide necessary background for those of you with little or no exposure to isotope geochemistry.  Next post I'll show you how the samples get loaded onto the machine and eventually we'll talk about how the machine actually goes from the samples to a useful result and what running the TIMS is really like.

The primary instrument we use in my research lab is a "thermal ionization mass spectrometer," which we refer to as "the TIMS" for short.  [Which, incidentally, has lead to several comical instances where people overheard me telling someone that I "date garnet" or "spend a lot of time with the TIMS" and then inquired about the romance in my life after assuming I was talking about a boy! lol] Breaking down the full name of the instrument actually gives a pretty solid overview of the instrument's purpose.  The TIMS uses high temperatures to ionize (break down into individual charged atoms) the sample, separates the ions by mass using an electromagnet, and allows us to measure the relative abundance of ions at specific masses to determine isotope ratios.  If that just went over your head, don't despair yet!  I promise upcoming posts will have pictures and likely use household objects as analogies to break this overview down into manageable parts.

First...a little general background on geochronology and why I use this crazy instrument.  As an 'isotope geochemist,' my goal is to figure out the age of each of my garnet grains and then use those ages to examine bigger questions about how mountains form and the surface of the Earth changes.  Figuring out the age of the garnet is possible because garnet includes trace amounts of a radioactive element called samarium (Sm) that decays to the element neodymium (Nd) at a known rate.  It takes 1.06x10^11 (106 billion) years for enough Sm to decay so that only half of the original amount is left (called the half-life).  Also, garnet is basically never 100% pure...it usually contains little bits of other minerals that we refer to as inclusions.  To borrow an example from my adviser...you can think of it as a chocolate chip cookie.  The cookie is the garnet and the chocolate chips are the bits of other minerals, or inclusions, inside the garnet.  Many of these inclusions contain a different ratio of  Sm to Nd than the pure garnet (just like the chocolate chips and the cookie base would have different ratios of sugar to milk).  Therefore, I use the TIMS to measure the Sm and Nd ratios in the pure garnet and in the inclusions.  Since the ratios are different and the rate of decay is known, when I plot the ratios for the pure garnet and the inclusions I can define a line between two points, called an isochron.
The slope of the isochron = The age of the garnet!

By the time I am ready to walk into the TIMS lab and start an analysis, I have already been working through sample preparation and clean lab chemistry on a single garnet grain for several weeks.  Those week of work result in a set of 4 beakers, each containing a single bead of dried goop about the size of a ballpoint pen's tip.  The four beakers contain the Nd from the pure garnet, the Sm from the pure garnet, the Nd from the inclusions, and the Sm from the inclusions.  Each isochron that results in an accurate age requires all four samples to run successfully on the TIMS, usually with only one shot at getting each one right. 

This is a very simplistic overview of geochronology and mass spectrometry, especially since there are entire courses on the principles of these areas of study.  Basically, once you understand that by measuring isotope ratios of Sm and Nd we can figure out the age of garnet, you understand the purpose of using a TIMS and one of my basic research goals. The remainder of my research examines ways that we can apply these methods to new materials that have never been dated or how the ages that I get tell us about the rates of metamorphism, when sedimentary basins open and close, how metamorphic conditions change over time, and much more.  

Monday, October 1, 2012

A Summer Summary..and on to Year 2!

So...you thought I'd totally forgotten about the blog, right?  It's not that I forgot..but that I forgot to prioritize writing a post amid what turns out to be the craziness of being a graduate student during the summer!  Goodbye summer vacation and hello full-time research!

To briefly catch you up from my long break from writing..here's a brief summary of the summer:

  • I finished my second semester, including completing a grad. course with my adviser in which I was introduced to the computer programs Perplex and TWQ.  Yippee for surviving my intro to thermobarometric modeling!
  • Flew home for baby brother's high school graduation.
  • Most of the summer I was working on a collaborative project with a visiting PhD student from University of Leeds, England.  He came and spent two months in our lab and I was assigned as his "buddy" and helped him learn lab techniques, design a plan of attack, run samples, etc.  Then once he left I have been finishing up the samples he did not complete.  Look for my first coauthored, peer-reviewed paper to hopefully be published in the next year!
  • I also worked on some of my own samples...dating several more "test" detrital garnets from Vermont that were used for a coauthored presentation given by my adviser at the Goldschmidt Geochemistry Conference in June.  I got to go along and attend Goldschmidt as well, which was in Montreal this year!
  • I was Maid of Honor in a wedding back home in July.
  • My family came to visit me in Boston in August.
Now I am officially a second year PhD student!  Although I must admit..being a second year is a lot more pressure than being a first year.  I now have more responsibility, a to-do list that is much longer than I could ever hope to accomplish and qualifying/comprehensive exams looming on the horizon.  Currently I am finishing the last of the samples still lingering from the summer's projects, as well as taking one course (basically an applied stats course for geologists with an intro to Matlab thrown in for good measure).  I am also writing an application for the NSF graduate research fellowship program and trying not to get too worried about quals in the spring.  Sound like fun?

PS- If anyone has awesome advice on applying for an NSF GRFP...I'd love to hear it!

Monday, March 19, 2012

Sustainability and Farm Shares

Lately I've spent a lot more time thinking about the health of our planet and what impact I want to have.  Now that I have moved across the country and have my own apartment, stipend and plenty of decisions to make, it is the perfect time to think about the lifestyle that I want to have now and in the future.

This past week I have been reading the book No Impact Man and briefly suspended my television hiatus to  watch the documentary Food, Inc.  No Impact Man is written by an author in NYC who did an experiment to see if he and his family could live for a year with gradually diminishing environmental impact across different categories, such as waste and transportation.  Food, Inc examines the way that Americans eat and where our food comes from, along with the potential implications of the current food system on the environment and our health.  Both of them are thought provoking and it is just the start of my research on the topic.  As a geologist I frequently here about or think about the global carbon cycle from an academic perspective, but I don't think I had stopped recently to consider my own lifestyle.

I have, however, settled on one step to take as a beginning.  As I was researching urban garden plots, reading the chapter of my book on sustainable eating, and talking to one of my peers, I stumbled upon the idea of joining a CSA program (CSA = community supported agriculture).  A CSA program provides revenue for farmers at the beginning of the season when they need it the most for planting and other costs by having consumers purchase a farm share at the very beginning of the season, typically sometime between February and May.  Then, throughout the growing season, the consumer who purchased the share receives a weekly allotment of produce directly from the farm that they support.  Not only is this a way of supporting local agriculture, most of the local farms offer organic or very close to organic produce and the carbon impact of shipping food across the country and around the world is eliminated.  In addition to vegetables, you can also find farm share programs that involve fruit, eggs, dairy, meat, or even fresh flowers.  Together my roommate and I purchased a small share from one of the farms here in Massachusetts (http://stillmansfarm.com/csa.htm).  From the third week of June through October we will get to pick up our shipment of fruits and veggies fresh from the farm at our local farmers market for roughly the same amount of money that we would spend on produce here in the city.  We get local, conscientiously grown food...plus an incentive to eat our fresh veggies!  I may live in the city, but I'm still a Midwestern girl at heart who loves the idea of garden fresh vegetables and eventually wants a goat and/or chickens someday.

I would encourage you to look for a CSA in your own area if you are at all interested.  They can be found across the country with a simple Google search.  Do something good for your local economy, the planet, and your own health.  If not, find another step to take to reduce your impact on the Earth and research the impact you are having on the planet.

Saturday, March 17, 2012

My First Garnet Age

It's been way too long since I've written a post.  I've saved up a nice long list of topics that I can write about and adventures from the last month and half but just haven't gotten around to writing the posts yet.  I'm hoping that this post will be the first of several over the next couple of days to get more or less caught up and whittle down my idea list.  Instead of going chronologically, I'm going to start with a science update...since that's the cause of my delay in writing anyway. :-)

There has been a lot of exciting science in the past month and a half since I wrote about my first trip to WHOI to use the SEM.  I'm balancing two classes (Geodynamics as well as "Thermodynamics and Kinetics of Tectonometamorphic Processes," which is taught by my adviser) and finally getting pretty close to being independent on most of my research procedures after learning several new steps these past couple of weeks.

The biggest push for research has come over the past two weeks.  This past summer when I did fieldwork in Scotland (see earlier posts if you missed the beautiful Scotland scenery!) I collected several samples and shipped them back here.  In November I sent two of those samples off for crushing and mineral separation and they came back roughly three weeks ago.  As I was in a meeting with my adviser just over two weeks ago, we were talking about research priorities and he mentioned that he would love to have an age for garnet from one of the samples ahead of his upcoming talk at the University of St. Andrews, Scotland on his European speaking tour but he wasn't sure if it was possible.  Normally taking garnet from raw mineral to an age takes us three to four weeks, with two weeks being the absolute fastest speed possible if everything goes according to plan.  I agreed to try and plotted out every step on a calendar, knowing that I would make it with just about 12 hours to spare if I succeeded.  It was also complicated by the fact that I have never completed some of the final steps, because I just hadn't gotten there yet with test samples.

So, basically the last two weeks were two solid weeks of lab work.  It included a second trip to Woods Hole to do SEM work on the Scotland samples (and incidentally learning how to change an SEM filament...), about a week and a half of 12+ hour workdays in the clean lab in my superhero get-up, two days of learning to load samples and how to load the mass spec., and two days of learning how to run our instrument.  (Eventually I'm hoping to write a series of posts to show you some of the basic methods and our instrument, the TIMS.)  Amazingly, my sample survived and I can finally say I have my first garnet age!!  Not only was this the first time I generated an age by doing the procedures from beginning to end, I made it within two weeks (with 11.5 hours to spare), it was a ridiculously small sample (I started with only 4mg of garnet...4 sand grains basically), many of the procedures I was doing independently for the first time or I was learning with supervision for the first time, and the result was right in the expected ballpark!  If you can't tell, I have been quite pleased for the last day or two.

Now that I have my first age under my belt, I can start testing and implementing some of my ideas for changes to the procedure to improve how our lab works with very tiny samples and for further method development on the new garnet dating system I am developing.  While I'm excited about my first data point, there are many improvements to be made and many more points to be gathered.  Onward in the pursuit of science.

Tuesday, January 31, 2012

Grains under the Microscope: A WHOI Adventure

About a week and a half ago I had the opportunity to visit Woods Hole Oceanographic Institute (WHOI) on the southern part of Cape Cod in Massachusetts.  I took a day trip away from my usual research at BU in order to gather some test chemical data on a couple of my detrital garnet samples.  I received an invitation from a research scientist at WHOI offering me the opportunity to try out a piece of equipment we do not have in our department at BU.

Before I describe what my day at WHOI looked like, let me give you some general background on the goal of the trip and the method that I was using for those of you who are unfamiliar with the SEM.  I traveled to WHOI to use a tabletop scanning electron microscope (SEM).  A scanning electron microscope uses a beam of electrons that bombard the sample.  When the electrons collide with the material being analyzed, different types of detectors can be used to provide information about the electrons that are scattered or energy that is emitted to learn more about the sample being analyzed.  The instrument I was using is smaller than most standard SEMs and is designed to be user-friendly, to take up less space, and to allow for analysis not just of polished, coated samples (which is the standard procedure) but also of rough, uncoated samples using a lower vacuum setting.  This makes this instrument an excellent candidate for analysis of my samples, since the grains do not have to be coated or polished, which would destroy them.  The tabletop SEM is equipped with two different detectors- a BSE detector and an EDS detector.  BSE stands for backscattered electrons and measures the electrons from the beam that are scattered and reflected by the object being analyzed.  It allows for the differentiation between heavy elements and light elements, since heavy elements scatter electrons more strongly.  From this differentiation, an image of the material being analyzed is generated using grey scale that can show surface detail or different mineral phases.  Below is an example from one of the grains that I analyzed at WHOI, though this particular grain is zircon rather than my usual garnet subject.
BSE image showing a zircon grain, analyzed at WHOI 1/20/2012
Besides BSE, the SEM can also do EDS analysis, which stands for energy-dispersive X-ray spectroscopy.  The electron beam hitting the sample can trigger the release of x-rays and the energy of the x-rays released is characteristic of the major elements that compose the object being analyzed.  This makes EDS useful for preliminary chemical characterization and mineral identification.  EDS results in a spectrum showing major element peaks and can also generate atomic and weight percentages for major elements using spot analysis.  Basically, we can get a general idea of the composition of the material being analyzed.

While I was at WHOI, I analyzed twelve different detrital garnet grains.  I used grains from two different locations in Vermont that we have been using as test samples throughout the method development process.  Three of the grains were from one location and the other nine were from a second location.  The sand collected at the second location contains detrital garnet of different colors, so I was able to analyze three grains of each color (red, orange, and pink) hoping to test the ability of the instrument to differentiate between garnet with different compositions.  When doing detrital work, it is important to be able to identify populations of similar grains that likely originated from the same general area and should be roughly the same age, since a single detrital sediment can contain different populations of garnet grains that originated from different locations and were affected by different conditions.  In addition to the garnet analyses, I also analyzed many grains of any other mineral that could remotely resemble garnet under the microscope from one of my other field areas to verify that garnet is not present in the sample.  Here is a picture showing how the grains were mounted for analysis.  The grains are still attached to this mount- they are just too small to see easily in the picture and blend into the carbon sticky tape.  The grain mount is sitting in a small weigh boat to minimize contamination.
Grain mount for SEM using carbon sticky tape
Just for fun, let me give you a look at what my day of research looked like.  My commute to WHOI started around 6:30am and involved two different subway lines, a Peter Pan bus, getting picked up at the bus station and a short drive to WHOI's Quissett campus.  I arrived around 10:00am and started learning how to run the instrument and by 11:00am I was running the instrument independently.  I then spent the next five to six hours (minus a lunch break) analyzing as many grains as possible and accumulating roughly 90 computer files between BSE images, EDS analyses, etc.  Then I took a shuttle bus to Woods Hole, where I ate dinner in an awesome little cafe while waiting for my bus to Boston.  (If you ever find yourself in Woods Hole, MA..I highly recommend eating at Pie in the Sky. It was delicious!)  After a bus ride and two more subways, I arrived home around 10:30pm.  It was a long and tiring day...but definitely worth it.

Here is one final picture, showing me running the SEM at WHOI.  Not only did I learn a new instrument and gather helpful information on some of my samples, I am learning how to be an independent scientist!
Me running the tapletop SEM at WHOI

Sunday, January 15, 2012

Away from Boston and Back Again: Christmas Break and a Research Update

Two weeks away from Boston for Christmas break, a week and a half back in Boston working on research without the distraction of classes, and the start of classes impending in the coming week.  It's been a busy month since I last wrote!

I went home to the Midwest to celebrate the holidays with family.  We had lots of laughter, family gatherings, time spent relaxing, present exchanges, and good memories.  Highlights included going to the Indianapolis Symphony to see the annual Christmas Yuletide show as well as having lunch with a good friend to see her new engagement ring!  While being home for two weeks was wonderful, all good things come to an end and it was back to Boston on January 4th.

The past week and a half I have been working on my research without the distraction of classes.  I must admit, having such large blocks of time for research tasks was productive but also pretty strange.  I'm used to doing 20 different things at once.  For example, a year ago I was student teaching full time in a rural high school and writing/defending a senior thesis at the same time and the semester before that I was taking 5 classes, including a couple upper level geology classes, while TAing for another 2 courses, working as a planetarium operator, working on research, and doing classroom observation hours.  The chance to focus on just research...well it's been a while since that chance came along.

It's been a fairly eventful week and a half in regards to research.  I have now learned most of the garnet dissolution and lab techniques that we use frequently and my first actual garnet samples should be analyzed within the next couple weeks... well as soon as the TIMS is working again.  For those of you unfamiliar with the TIMS, it is the main analytical instrument that our lab uses to generate chemical data on garnet.  I don't want to get into all of the particulars of the machine's operation or purpose at the moment (I'll save it for a more extensive post with pictures to illustrate) but suffice it to say that the solution for fixing the instrument involved disconnecting all of the electrical connections and probes, rolling a 900+ pound magnet away from the instrument, and using heating pads, internal heating elements, and insulating blankets to literally bake the instrument to high temperatures to burn off any accumulated debris from years of use.  I got to help our lab tech. go through the steps to prep the instrument for baking and learned a lot about the instrument in the process!  I have also been doing major sample preparation in anticipation of a trip to Woods Hole Oceanographic Institute (WHOI) this coming Friday for preliminary chemical analysis.  Keep an eye out for a post next week on my adventure to Woods Hole!