When the temperature was ridiculous.

Some days, weeks, and even entire months science doesn't go according to the nice and neat plan.  I tend to share some of the exciting and fun things that happen around here, but not all days are quite so joyful.

Instruments break.  Clean labs break.  Meters for measuring pH break.  Sometimes they all decide to break at the same time.  Welcome to May and June of 2014 in the Baxter lab!

This is the reading on the thermometer in the clean lab today (Photo credit to my labmate Jamie Kendall!).....

Yes..you read that right.  It's 95 degrees (Fahrenheit) in the clean lab. The clean lab is supposed to be at a tightly controlled 68 to 70 degrees F in order for chemistry to continue!  Luckily, I could spend the day paper writing and crossing my fingers that the new air conditioner gets installed on the roof via crane soon!

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.  

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.

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

Metamorphosis of a Superhero

Spies go undercover, adopting a new set of clothing and a new appearance in order to fulfill their missions.  Superheroes have brightly colored suits, capes, and a wide array of weapons and gadgets at their disposal while they save the day.  Geochemists often have their own equivalent of the superhero costume or undercover spy clothing- they have clean lab gear!

Several weeks ago I shared a picture drawn by my best friend that shows me as a superhero named GeoKate.  Here it is again in case you missed it the first time:

This picture along with questions from several people about what I have to wear when working in the clean lab have inspired me to present a real-life view of GeoKate, who by attending grad. school is in training to become a geochemistry superhero.  Enjoy!

The Metamorphosis: From Ordinary Grad. Student to Clean Lab Superhero
Upon entering the outer room of the clean lab, the heroine leaves behind the tools of her everyday life (keys, phone, shoes, etc) and prepares to transform.  Winding her way deeper into the lab, she encounters the cloak room, and the metamorphosis begins.

1)  Shoes- Lab shoes not only prevent acid from damaging the heroine's feet, but add a stylish touch to the superhero uniform.

 2) Hair net- A stray hair in your lab beaker is definitely not acceptable.  Neither is having your hair in your face while you're flying.

3) Hood-  A key part of obscuring your identity, since it makes everyone in the lab look identical from most angles.

 4) Lab coat-  Besides the practical use of keeping her clothes clean while fighting crime and dissolving rock, it nicely doubles as a cape while in flight.  It also confuses all of the various evil doctors and villains who often use lab coats as their standard uniform.  They don't expect a superhero to wear one!

5) Face shield/goggles-  GeoKate is modeling the face shield here but most of the time wears the less extreme goggle option.  But sometimes you just need the extra protection and a bug guard while flying!

6) Gloves- Blue nitrile gloves.  Definitely an up-and-coming fashion trend for the functionality conscious.  No germs, no mess, and a splash of color that matches the shoes. Not to mention no fingerprints.....

  Voila! The metamorphosis is complete.  Now...off to save the day! (or learn more about garnet...)

Grains of Sand

About a month ago I told you about my piles of sand.  Now I am headed for single grains of sand and you are invited to follow along with my next science installment!

My last science installment followed the steps involved in generating several vials of sand with magnetic properties close to those expected for my mineral of interest- garnet.  This process narrows the search field, but unfortunately never yields a vial of pure garnet.  That's where the next step comes in.

The next step is known as hand-picking.  It takes place under a stereoscope, which looks like this:

Stereoscope on and ready to go

Basically, it's a microscope that allows the user to examine three-dimensional samples under varying magnifications and light intensities.  This particular scope is also outfitted with a digital camera for taking pictures of the individual sand grains when necessary.

The samples, which can be seen in the vials to the right of the scope above, are dumped into a weighing boat (the blue plastic dish the vials are in- above) or a clean glass dish.  The dish and sample are placed under the stereoscope.  Then I have to use the magnifying powers of the stereoscope, very fine tweezers, and my mineral identification skills to sort the garnet grains from all of the other grains of sand, proceeding one grain at a time.

PTFE-coated Tweezers, ink pen and lab notes for scale

I have two pairs of tweezers- one made from non-magnetic stainless steel and the other pair coated in PTFE (Teflon).  Both are considered needle-point and are essentially some of the finest tipped tweezers available.  They have to be...I am using them to pick up individual sand grains!  Why two pairs you ask?  The pair coated in Teflon is intended only for use with my detrital garnet grains, to minimize the exposure of the grains to unnecessary metal.  Contact with metal objects could, theoretically, contaminate my samples and skew my results since I am working with such extremely small sample volumes.  I am pretty sure that any potential impact of metal contact will be mitigated by later processing, but it never hurts to avoid the potential problem altogether when possible!  

Ultimately, each grain of garnet is individually picked out of my piles of sand using the tweezers and placed in a new vial containing only garnet from a single sample.  Generally, garnet is fairly easy to identify beneath the stereoscope's magnification, since it is pink to red to reddish brown.  Most of the other minerals that end up with it when grouped magnetically are nowhere near this color spectrum.

Hand-picking continues until I have gathered a vial with enough garnet to be analyzed.  This can take quite a bit of time, since each grain is selected individually.  Once enough grains are selected, it's off to the clean lab!  More on those adventures will be coming soon..... 

Of course, this is nowhere near an ideal system for mineral separation yet.  My original sand contains an extremely large volume of two minerals known as quartz and feldspar.  They are so abundant, that although magnetic separation should keep them far away from the garnet, they have permeated everything and to make matters worse, the feldspar is pink!  I am currently researching additional processing steps to add to our current mineral separation methods, such as heavy liquids and/or a water table, to eliminate this problem. Hopefully there will be posts in the future about new processes and procedures that I have added to our lab's capabilities to deal with these issues.