Lab life: the cleanroom, the machine, the clothes, the work, and the fun

Last week was all about me, but this week is all about the lab. As I dove into in my About me bonus, I am a paleoceanographer, paleoclimatologist and a geochemist. Specifically, I use certain elements, mainly Mg/Ca ratios, to reconstruct past oceans and climate. To do that, I need a lab. But not just any a lab; I need a lab with a (very) cleanroom, a very nifty inductively coupled plasma mass spectrometer (ICP-MS), some wonderfully fashionable and functional clothing, and of course, a lot of interesting and exciting work. Here at INSTAAR, we call that lab the ICP-MS Trace Element Lab. And it’s in this lab where all my PhD dreams will come true (or explode catastrophically).


The cleanroom

What’s a cleanroom? Well, a cleanroom, is a room that limits the introduction of contaminants (i.e. dust, airborne particles, pollutants, etc.) through engineering controls to preserve process or sample integrity. Why do I need a cleanroom? The samples I work with are very specific to a source (where the sample came from) and a time (when the sample was “made”). This means that all the elements stored within a sample will be different from a sample taken somewhere else. The elements will also be different from the environment, let’s say, in a geology building. If a processing or dissolved sample (i.e. a sample that is being prepped for analysis on a machine) sits out in the un-protected geology building environment, it can uncontrollably “take in” or react with the set of elements its composition differs from because of its vulnerable state. This isn’t good. A contaminated sample will no longer accurately represent its source and time, thereby possibly changing the history the geochemist (i.e. me) will try to discern from said sample. This is where the cleanroom comes in; it limits sample contamination by controlling the environment.

IMG_5012

A cleanroom to a geochemist is like a operating room to a surgeon; IT’S VERY IMPORTANT. It’s where we work our science magic (or sometimes where our dreams are crushed). Without getting too technical, my samples need to remain as clean (i.e. not contaminated) as possible through crushing, cleaning and dissolving steps (i.e. prepping for analysis) in order to accurately represent its history. Engineering controls, such as air filters, negative room pressure, laminar flow benches, and even coated metals (or better yet, metal substitutes) are used to limit sample contamination. Because we’re scientists, we have all sorts of checks to determine if contamination did indeed occur, such as: running a acid blank (no sample) test prior to using said acid to dissolve a sample or analyzing acid blanks during a sample run to determine if contamination occurred while dissolving samples. However, even in a cleanroom, contamination does still occur.


The machine

What’s an ICP-MS? It’s a mass spectrometer with energized plasma that ionizes a dissolved (liquid) sample to analyze a set of specific elements. Decoded: an ICP-MS will take a dissolved sample, analyze it and report a specific suite of elements. The suite of elements the ICP-MS reports depends on a couple things, mainly: the analytical precision and sensitivity needed to complete a run (some samples are smaller than others and thus require more precision and sensitivity to be successfully analyzed) and the interests of the researcher using the machine. I could go into all the physics behind this glorious machine, but as I myself am still learning them… I won’t. Just know this: Mg/Ca are the elements I’m mainly after and I will use this machine to find them. I will also analyze my samples for other elements, but that is a discussion for another day.

The ICP-MS is housed in an adjoining room to the cleanroom, and like the cleanroom, is a vital part of the lab I will be working in throughout my entire PhD career.


The clothes

IMG_5010I’ve been talking a lot about the air contamination, but contamination doesn’t just come from the air; it can also come from particles trapped in clothing. Because outside clothes and shoes, are well, from the outside, they must be covered at all times when in a cleanroom. In most geochemical labs, the coverings include a stunning white tyvek suit and booties. This makes us cleanroom geochemists the most stylist of the geology bunch.

Fashion joking aside, personal protective equipment (PPE) is a huge and vital part of any lab. The main function of the tyvek suit and booties is to protect the cleanroom from outside contaminants, but a secondary function is that it can protect one’s body from minor chemical spills. Gloves and googles/glasses top off the glorious cleanroom ensemble to protect our dainty hands and seeing organs–safety first. My PPE is designed to handle less hazardous material as the chemicals I work with are very dilute; however, I do still handle chemical stock solutions and other concentrated chemicals, so I still have to be very careful in the lab.


The work

Of course, working in any lab requires a significant amount of training (and often a very large learning curve). From safety training, to process training, to day-to-day maintenance, to just finding the damn pipette tips… a new labbie could spend anywhere from a few weeks to an entire year getting comfortable in a new lab. When a lab contains a cleanroom, one must follow an even higher level of scrutiny. Lucky for me, I worked in a similar cleanroom setting as an undergrad, so some of the basic concepts (i.e. upkeep, storage, cleaning, safety) are review for me. Unlucky for me, lots of other parts of my new clean lab (i.e. anything and everything foram and ICP-MS) are completely new to me, and it will still take some time (and lots of mistakes) for me to get 100% comfortable.

Lab Hazard Rating System

Via “Piled Higher and Deeper” by Jorge Cham, http://www.phdcomics.com

My PhD will likely be lab heavy in the first couple of years. Some days, I won’t leave the lab (probably not by choice, but hey, when in PhD mode, one must PhD). Others, I’ll run far, far away from it (hopefully to be super productive reading and writing, but more likely I’ll be looking for beer). During my PhD, my lab work will include all sorts of tasks: foram picking, crushing, cleaning, dissolving and analyzing; chemical dilutions; lab cleaning and organizing; beaker/cup cleaning; ICP-MSing (i.e. sweet talking the inductively coupled plasma mass spectrometer); and many, many more. The foram tasks will take by far the longest, and most of those tasks require use of the cleanroom. Use of the ICP-MS will also be somewhat time consuming, especially when the machine is being difficult (as I write this, my advisor and I are trying to keep it from overheating so we can finally run some samples). However, I’ve spent my summer learning a lot about the machine, and hopefully by the time my own samples are ready to be run, I’ll be a super knowledgable (or at least semi-knowledgeable) ICP-MSer.


The fun

But life in the lab goes beyond the lab, the clothes and even the work; you learn along the way to have a little fun and to make a little fun of your mistakes or tragically embarrassing situations. To let you in on the “fun” part, I’ve decided to write about some of the funny situations you could find yourself in while working in a cleanroom. So, without further ado, I present:

You know you work (or have worked) in a cleanroom when…

  • You can replicate the delicate dance of putting on and (the often more difficult task) of taking off your tyvek (“bunny”) suit and shoe coverings in your sleep
  • You’ve fallen over trying to get your limbs out of your tyvek suit (probably in front of your advisor or professor or a very important world-renown scientist)
  • You’ve made the mistake of completely suiting up after drinking five cups of coffee… and not running to the bathroom first
  • You’ve found the “slippery” part of the cleanroom floor and know first hand what it’s like to feel as if your life is about to end (since you’re holding very delicate samples, and/or scary acids, and/or your advisor is standing right behind you)
  • You don’t care what you wear to work because nothing’s more fashionable than tyvek white
  • You’ve tried to sit down on a normal office chair while donning your tyvek suit and have gone flying off the chair Christmas Vacation sledding style
  • You’ve made the mistake of leaving your notes on the wrong side of the cleanroom and not realizing it until after removing all your fancy cleanroom clothes
  • You’ve made the mistake of leaving your notes in another room and not realizing it until after completely suiting up
  • You know what it feels like for people to think you’re about to get into some serious shit… but you’re really just going in the lab to clean some beakers
  • You look like a giant marsh-mellow… and like it
  • You know the struggle of trying to get your cell phone out of your back pocket once you’re already suited and zipped up
  • Your favorite time of the week/month is when you get to rip off the nasty sticky pads at all door entrances to reveal the brand new sticky pads underneath
  • You know what it’s like for something to come up in the lab where you need help from your more experienced advisor, lab manager or the lab’s grad-student/postdoc extraordinaire and have the internal debate about whether you should completely un-suit to hunt him/her down… or shamelessly text him/her until he/she comes to your rescue
  • You get angry over someone using the tyvek suit CLEARLY labeled with your name

#cleanroomproblems

About me bonus: what I do, why I do it and the basic science behind my PhD

By now, most of you are well aware of my love affair with geology. However, some of you may still not exactly understand what I do or why I do it or have any idea what my upcoming PhD focus means. Because my work will never be an easy explanation for those unfamiliar with what I do, I decided to take this week to describe as best I could (and as un-jargony as possible) what I do, why I do it and the basic science behind my PhD. Eventually, I’ll add or link a shortened version of this to my about me (hence the title), but I felt these words were probably best served first as a standalone post.

As with many geologists, I study the past. I do this for a variety of reasons. First and foremost, I enjoy it. It’s exciting for me to dig into Earth’s history and learn something we didn’t know before or better understand something than we did before. Second, Earth is extremely complex. Studying modern-day change is vital to understanding the complex relationships of Earth systems, but studying the past, and all its glorious “natural experiments,” allows scientists to explore Earth dynamics beyond modern constraints. The past was different than today, and understanding the differences between ancient and modern Earth is extremely important. Lastly, studying the past allows scientist to apply past analogs to future scenarios (i.e. using the past to inform the future) not only in an effort to predict possible outcomes, but also to help the world prepare to face those outcomes. The latter point is the most important to me. We live in a rapidly changing world where human actions have a resounding impact on Earth’s future. Understanding how our planet responded and reacted to past changes, is our greatest hope to predict, plan and prepare for (and in an ideal world, limit) the negative impacts stemming from modern human actions on the complex Earth system.

climate comic

Extremely relevant Joel Pett cartoon, USA Today (2009)

There are lots of ways to study the past, which is why there are lots of different types of geologists (and paleo-[add your science here]-ists). There are geologists who study large, massive structures in ancient formations that are visible for miles away, and there are geologists who study the chemical make-up of rocks and minerals that can only be be discerned after hours of laboratory prep and machine analysis. Some geologists focus on deep time, while others focus on more recent events. Then there are geologists who wander all around the geologic boundaries, putting on all sorts of geologic hats in an attempt to better understand our wonderfully complex planet. Pick any topic and any time period (or even multiple combinations as insane as it may seem), and I guarantee you there’s a geologist somewhere dedicating his or her life to that very geologic niche.

In the spectrum of geologic possibilities, I am a paleoceanographer, paleoclimatologist and geochemist focused (for now) mainly on the more recent geologic past. To decode that geological jargon: I study ancient (but not too ancient) oceans and climate, and I use elements (i.e. chemistry) to discern past events (i.e. geology). Simply put, I’m one of those that wears lots of hats. And to make it even more confusing for you, all of the aforementioned words I used to describe myself as a geologist don’t necessarily make me a geologist at all. Paleoceanographers and paleoclimatologists come from all walks of scientific life. Some are geologists, yes, but many are atmospheric and oceanic scientists, or physicists, or chemists, or even biologists and statisticians. And like the word spells out for you, geochemists are often trained chemists “dabbling” in the world of geology. I will spend the next five years dipping my toes into geology… and all the other wonderful sciences that play a role at the cross-section of paleoceanography, paleoclimatology and geochemistry. Needless to say, I will be very busy as PhD student (gathering lots of pretty hats).

g. ruber foram

An example of fossil foraminifera. See source for detail: Thirumalai et al. (2014), Globigerinoides ruber morphotypes in the Gulf of Mexico: A test of null hypothesis. Scientific Reports 4, 6018. doi: 10.1038/srep06018

Now for the technical stuff. For my science readers–this will probably be easy for you to follow. For all my other readers–I’ll do my best to de-jargon. During my PhD, I will be using (i.e. picking, processing, dissolving and analyzing) fossil foraminifera (a marine protist with a calcite shell–here’s Wikipedia) that have been preserved in ocean sediments to determine and understand past ocean and climate states, changes and relationships. How will I do that?: magnesium (Mg) and calcium (Ca). Mg/Ca ratios can be used as a paleo-proxy (i.e. recorder of the past) for temperature. Simply (and without sending this post down the rabbit-hole of Mg/Ca relationships), the amount of Mg in a calcite mineral relates to the temperature at which that mineral was formed; the more Mg that is in a calcite, the higher the temperature was at the time of formation. In the case of formanifera, or forams, the temperature recorded by a calcite shell is the temperature of the sea water surrounding the foram at the time of shell formation or its calcification temperature. Pretty cool, right? (Yeah, I think so). Measuring Mg/Ca ratios in fossil forams allows scientists to calculate past ocean temperatures! (I know you’re as excited as I am). The exact Mg/Ca-temperature relationship can be dependent on other factors, including foram species, habitat, salinity and even dissolution effects (all things I won’t get into here as it would turn this post into a lengthy research project), but some very, very smart people have developed a myriad of calibration equations (i.e. equations that directly relate Mg/Ca ratios to temperature) to isolate the temperature signal.

Phew. If you made it this far–HIGH FIVE!

Now, some of you are probably wondering exactly how ancient ocean temperatures are going to help me determine and understand past ocean AND climate states, changes and relationships–and that would be a very fair thing for you to wonder. The ocean plays a major role in the Earth climate system, which also includes very important things such as the biosphere and the atmosphere. A perturbation in one part of the system often affects the other parts of the system. For example, a major shift in surface temperatures on Earth will cause a shift in ocean temperatures, which will cause a change in atmospheric winds and weather, which will affect the plants and animals dependent on all those things (…so on and so forth). Understanding the whole Earth climate system requires knowledge of all its parts. And knowledge of one part can also lead to insights on others. I choose to study the ocean because it’s a part of the Earth climate system that we probably know and understand the least about. And while the ocean is only one piece of the giant, complicated climate puzzle, its piece and its close connection with other pieces can tell us a lot about the past. So really, my ancient ocean temperatures will actually tell me a lot more than a simple reading on a thermometer. For those curious about exactly what my PhD project will be, I’ll probably reveal more about that later down the road. As a new graduate student, I’m focused mainly on catching up on the slew of wonderful Mg/Ca-foram literature (I still have a lot to learn), and while I have a pretty good idea where my project is going, things can always change.