Category: graduate school

Temporal Disconnect: An Underwater Oceanographic Institution?

Martha’s Vineyard oceanview, Cape Cod, November 2008.

I was walking along the beach today in Woods Hole here on Cape Cod. I wanted some fresh air and felt like collecting some seashells. You always find the best seashells in the winter. There’s no one else on the beach, usually, so the biggest, most beautiful seashells will just be waiting for you there on the sand, perhaps tangled in some seaweed. As I walked the beach and looked for shells, I thought about how in the next century or two– at most– all of Cape Cod will be underwater.

I find it somewhat ironic that Woods Hole Oceanographic Institution (WHOI)– one of the leading research institutions studying oceans and climate change– will be one of the first places to go underwater once sea level rises, as it is currently doing and will continue to do over the next hundred years or so. The institution is built on the low-level glacial till of Cape Cod, and most of the scientists have offices with an ocean view. In the summer the scientists and graduate students often go down to the beach for a quick swim. Building an oceanographic instituion on the ocean makes sense, but if WHOI scientists and trustees were smart they’d begin investing in some property in the hills of New Hampshire. Why? Because that’s where the new oceanfront property will be not so long from now.

The scientists here at Woods Hole are very environmentally aware. The scientific parking lot is cluttered with bicycles and compact hybrid cars, a great contrast to the Land Rovers and SUVs that fill the nearby Martha’s Vineyard Ferry parking lot. Most people you encounter here acknowledge that climate change is occurring and that sea level will rise significantly in the near future.

Almost everyone here would agree that Cape Cod will be one of the first places to go underwater when sea level does rise significantly. However, no one seems to worry about the location of the oceanographic institution. At least, they don’t worry about it on a day-to-day basis. The scientists take their lunchtime strolls along the beach and play with their expensive mass spectrometers and PCR machines in their multi-million dollar labs. No one seems too worried about having to move all of these fancy labs and scientific equipment once sea level rises.

I am sure that at times Woods Hole scientists must wonder about what will happen to the oceanographic institution once Cape Cod is underwater.Yet, it is difficult to really worry about the institution on a day-to-day basis, even for those scientists who are actively studying climate change. I’ll speak now for myself: while I intellectually recognize that the sea is rising– and rising fast– I cannot wrap my mind around the effect of sea level rise on my own life. When I look at the ocean, I don’t see it rising. One day’s ocean does not appear different from the next day’s. Sea level rise occurs fast on the geologic timescale but still occurs quite slowly on the human timescale.

Human minds have not evolved to think on geologic scales. We are very well-adapted to thinking on the scales– both physical and temporal– that apply to our own short lives. If one cannot actually see the sea rising or anticipate it rising significantly within her own lifetime, it is difficult to become alarmed. One may have minor concern for one’s descendants, but that gut reaction of “Wow! The sea is rising, so I’d better run away” just doesn’t happen for an ocean that rises on the order of millimeters per year. You just can’t see the change occurring nor anticipate- in a gut way- its future influence on your life.

Honestly, I think this is why the issue of sea level rise and climate change is so difficult for many people– myself included– to become worked up about. I am a first-year graduate student now in the program at Woods Hole. I will graduate in four to five years**. Very likely, Woods Hole will not be underwater in five years. After I graduate, who knows where I may end up? So, I find it challenging to become concerned about sea level rise here on Cape Cod, at least in my daily life and routine. Once the waters are lapping at my office door, then I’ll become alarmed.

Technology Anachronisms in Science

MacDiff program running in a Mac Classic environment emulator on my Windows XP netbook, January 2011.

Ever since I starting doing geology research back in 2003, I have encountered technology anachronisms in science. I find these technology anachronisms intriguing, humorous, and- sometimes- frustrating. Often, the challenge of using technology in science is not keeping up with the latest-and-greatest technology but rather remembering or learning to use very old, outdated technology.

What is a technology anachronism? Basically, this is a piece of technology (e.g. a computer, a data reduction program, a mass spectrometer) that is old and out-of-date– sometimes wildly so– but which is still in regular use for any of a variety of reasons. A good example of a technology anachronism is the soon-to-be retired Space Shuttle. My senior year of high school, I remember reading a 2002 New York Times article titled “For parts, NASA Boldy Goes… on eBay.” Basically, in 2002 (and probably in 2011) the Space Shuttle was still using early 1980s computer technology. In order to keep the shuttle computers in good repair, replacement parts were sometimes needed. The problem, of course, was that 1980s computer parts were hard to come by in 2002. Thus, NASA would buy replacement computer parts on eBay and any other place they could scavenge them from.

So why did NASA go on eBay rather than just outfit the space shuttle with new computer systems? Well, you’ll have to ask NASA about that for an official answer, and I’m sure they did make some updates to the shuttle’s computer technology. However, I imagine that designing a space shuttle– even just part of a space shuttle– is such a long, rigorous process that it is more practical to maintain the outdated but tried-and-trusted technology rather than overhaul with new technology that would require significant energy to design, test, and implement.

About a year after I read the NASA article, I started participating in science research in a geochemistry lab down at Florida State University (FSU). I went down to FSU to work as a summer intern. For my project, I measured hafnium (Hf) and neodymium (Nd) isotopes in some post-shield basalts from Hawaii. I measured Hf isotopes on a very old mass spectrometer* that had been specially modified for the task. The computer that was hooked up to the mass spectrometer was early to mid 90s in vintage. Much of the running of the mass spectrometer was done by hand (physically pushing in the samples, initial settings and calibration), but the computer did have a program for measuring the isotopes. The computer program was difficult to use and full of glitches. I forget what code was used, but I think it was an old FORTRAN code that had been programmed by a graduate student or technician way back when. The results came out on an old dot matrix printer with the holes on the edges to move the paper along.

More recently, I have encountered a technology anachronism in the software program I am using to identify minerals in X-ray diffraction (XRD) scans of rock powders. To identify minerals, I am using a program called MacDiff. This is a great XRD analysis program– it’s free and works really well for basic mineral identification. There are other, very expensive programs with larger mineral databases and more capability. However, I don’t require this much analysis for my thesis, so MacDiff is fine. There is just one problem with the MacDiff software: the program has not been updated since about 2000. The program also only works on a Mac, but even that wouldn’t be a huge problem if it worked on a recent Mac. Actually, the program can only be run in the Mac Classic environment.

There are two options for working with MacDiff. The first option is finding an old Mac computer that can run the Mac Classic environment. This is not too difficult as many scientists have old Mac computers lying about, and worst case scenario you can always buy an old Mac fairly cheaply off eBay. The second option, which I decided to pursue, is to set up an emulator environment so that you can run the Mac Classic environment in a window on a modern computer. Setting up an emulator is a little bit tricky (well, for me anyway), but I had a computer savvy friend help me figure it out. Running MacDiff through an emulator works well with just a few problems. The emulator tends to crash if you do certain things in certain orders, but I’ve managed to figure out ways around the problems I’ve had with the emulator. I really wish that a scientist or programmer would update the MacDiff code so that it would run on a modern computer, but that coding represents a significant time investment, so it probably won’t happen anytime soon.

I have encountered countless more technology anachronisms in scientific research. In my experience, there are several reasons why technology anachronisms exist:

1. Money:
There can be a high cost in replacing technology. Scientists cannot afford to replace very expensive equipment– such as million dollar mass spectrometers– often. For example, here at Woods Hole Oceanographic Institution there is an ion probe** that is from the late 1970s. There is also a newer, fancier ion probe. However, since ion probes are so expensive and in demand, the old 1970s one is still run regularly.

2. Time and Effort:
Replacing technology and becoming used to new technology takes time, which scientists have far too little of these days. Sometimes, it is faster and easier to keep the old technology limping along rather than take the time to transition to new technology. As an example, if an extensive code has been written in outdated FORTRAN, many scientists prefer to keep working with the pre-existing FORTRAN code rather than take the time and effort to re-write the code in a new language.

3. Comfort:
Humans, scientists included, are often resistant to change. Like NASA space shuttle operators, scientists like working with tried-and-trusted technology. Sometimes, this means clinging onto a computer or code or machine longer than they should. Older scientists in particular can sometimes be unfairly critical and suspicious of new technology.

4. Compatibility:
Sometimes, using older technology is really the only option. For instance, if you are using an old ion probe you may need to use an old computer in order to be able to talk to that old ion probe. Similarly, if you are using a group piece of technology– such as MacDiff– that you cannot update on your own, then you may be stuck with old technology unless the whole research community makes an effort to update the technology.

There will always be anachronistic technology in science, if only because the pace of technology development is so rapid these days.This is especially true when it comes to computers. The day you buy your shiny new laptop, this laptop is already out-of-date. New and better computers and computer-like gadgets– smartphones, electronic book readers, tablet PCs– are constantly being released. New software programs (Microsoft products, internet browsers, blogging platforms) come out every couple of years, and updates to these commonly-used software programs come out all the time.

So, whatever technology you purchase for your science, it’s likely to be out of date by the time you install it in your laboratory.

*For mass spectrometry geeks, the machine was the Lamont Isolab 54 Secondary Ionization Mass Spectrometer (SIMS).

**For ion probe geeks, the older ion probe is the IMS 3f. WHOI also has a IMS 1280.

A Million Random Digits

First page of random digits in “A Million Random Digits” book. Image taken from Amazon.com.

Earlier this evening I met up with three classmates (all girls, by the way; my statistics class is about 90% female) to work on programming our latest statistics homework into MATLAB. Working in a group is easier as four pairs of eyes tend to catch code errors faster than one pair of eyes. Also, we can eat Chinese food and giggle and have fun as we work.

One of the things we had to do this evening was use the “rand” function in MATLAB. This function calls upon a computer algorithm that generates random– or really pseudorandom since they’re calculated by a computer– numbers. The “rand” function calls upon a random number between 0 and 1 as a default, though you can tell it to use other ranges.  Random numbers are very important for many types of statistical analyses and numerical simulations. These days, many computer programs, such as MATLAB, have pseudorandom number generators built in. For most types of applications in mathematics and science, a pseduorandom number is nearly as good as a random number.

But what if you need actual random numbers?

And how did people generate random numbers before computers became fancy enough to generate pseudorandom numbers?

We started wondering about these two questions this evening. During our discussion about this, one of my classmates said, “Have you ever heard of that book that is nothing but random numbers?”

Of course, we had to immediately google this book, procrastinating our coding for a few minutes.

Cover of the book “A Million Random Digits.” Image taken from here.

Indeed, there is a book that contains nothing but a short introduction and then page after page of random numbers– 1 million of them, in fact! The book is titled “A Million Random Digits with 100,000 Normal Deviates.”

This book was first published by the RAND Corporation in 1955. If you go to the RAND website about the book, you can actually download the book for free. The text parts of the book come as PDF files and you can download the million random numbers as a data file. In the old computing days, you could order punch cards with these million random numbers. If you want a hard copy of this book (magicians and mentalists– wouldn’t this book make a great prop for your shows?), you can order it either from the RAND website or from Amazon.com.

A book of random numbers might seem incredibly boring; you wouldn’t want to read this book cover-to-cover, that’s for sure. Yet however boring, this book is very useful. Even though pseudorandom number generators are much easier and more commonly used these days, there are still times when mathematicians and scientists need truly random numbers. And for this, the RAND compilation remains the largest published source of random digits.

You might be wondering how these million random digits were generated. If you read the introduction to the book, the method of number generating is explained in detail. Basically, the numbers were generated on a roulette wheel. So, if you went to Las Vegas and played roulette for days (years?), you could generate a million random numbers, assuming there are no biases in the wheel.

Roulette Wheel. Image taken from wikipedia here.

The wheel that was used to generate the random numbers was actually an electronic roulette wheel that was hooked up to a very early computer. At first, the numbers looked random, based on various statistical tests. However, after awhile the RAND employees evaluating the randomness of the numbers realized that their electronic roulette wheel wasn’t perfectly random– there was some drift over time, probably as the machine aged and changed slightly in operation. You can read more about the biases of the electronic roulette machine here. To make the numbers truly random, the RAND employees- to put it simplistically- shuffled them up a bit.

I think this book of numbers is really great. I’m even tempted order this book as a coffee table book. I can just imagine my in-laws (who already think I’m strange) picking this book up off the coffee table and wondering why on Earth we have a book of numbers. I can’t quite justify the purchase (the book is about $70) on my graduate student budget, but perhaps I’ll order it sometime in the future.

Many people find this book of numbers both interesting and amusing. If you go to Amazon.com and read the reviews for this book, there are a plethora of hilarious ones. Below are a few reviews I found particularly entertaining:

“The book is a promising reference concept, but the execution is somewhat sloppy. Whatever algorithm they used was not fully tested. The bulk of each page seems random enough. However at the lower left and lower right of alternate pages, the number is found to increment directly.”

-B. McGroarty

“Such a terrific reference work! But with so many terrific random digits, it’s a shame they didn’t sort them, to make it easier to find the one you’re looking for.”

-A Curious Reader

“I definitely prefer books like ‘One million sequential numbers’ as the story always steadily progresses. By comparison this book is just so and so.”

-Devide Cerri

“For those who thought that ‘Atlas Shrugged’ could not be surpassed, here Rand refutes all doubters and utterly tops that opus in a style so rarefied and refined that words themselves have been transcended, with the essence–no, the ethereal, mystical quintessence–of Rand’s philosophy expressed as its ultimate ur-truth of a million unrelated symbols floating forever in pure mindless randomness. Rand’s myrmidons will find this most congenial, and I recommend that they spend the rest of their days reading this ne plus ultra masterpiece, meeting 24/7 in pure white Randian temples, there to pontificate and meditate on this wonder and that way stop bothering everybody else.”

-George Zadoronzy

“Wow, what can I say. A very insightful novel. The way the author manages to manipulate those numbers was wonderful.

SPOILER ALERT!!!

I have to admit, there were many twists that I didn’t expect, especially when he decided to follow up 9238399 with 2883002. I have to admit, the beginning was rather slow, but it began to pick up pace somewhere on page 7. My only regret is that there isn’t a sequel, because the author left it at a cliffhanger.

At times spontaneous, blunt, and errant, this is a book that you can definitely share with your friends.”

-Anna Huynh

A Conversation with My Doctor

Last weekend I made a quick trip down to Tennessee to visit family since my great-grandmother recently passed away. I flew out of and back into Boston Logan airport. Before I headed back down to the little village of Woods Hole, I went to visit my doctor at MIT Medical– a facility that serves MIT staff, students, and their families.

I had a somewhat entertaining conversation with my doctor. The conversation went something like this slightly stylized version:

*****************
Doctor: So, tell me what’s bothering you.

Me: Well, my left hand is somewhat numb and painful. I think I’ve just been working under the microscope for too many hours, but I thought I’d visit just in case I’m dying of some horrible disease.

My doctor laughs softly then catches herself and tries to look more serious.

Doctor: Is your hand numb everywhere?

Me: Somewhat, but it’s mostly the two outer fingers.

Doctor: Huh. Well, I would ask you if your hand felt better on weekends, but you probably work through the weekend.

Me: Yes. Well, except this past weekend. And my hand does feel a little better.

Doctor: Oh good. Did you do anything fun?

Me: My grandmother died.

Doctor: Oh. Well, you said your hand is feeling better?

My doctor does various reflex tests and decides that I am probably putting too much pressure on a nerve at my elbow, probably by leaning on my elbow when using the microscope.

Me: Great. I’m not dying of any terrible disease. Just of my thesis.

Doctor (laughing): I guess you could say that. Well, I recommend that you work fewer hours under the microscope and take some weekends off.

The blood drains from my face, and I start twitching nervously.

Me: I’m a 5th year.

Doctor: Oh. In that case, try putting a pillow under your elbow.

*****************

Don’t worry. I’ve switched to another microscope and my left hand is doing much better. I can almost feel all my fingers again. Besides, in a few short months all this scientific perspiration will pay off.

However, I am looking forward to being finished with graduate school and having a better life balance. Perhaps I’ll even have all of my fingers.

Scientific Perspiration

Note that I originally wrote this essay during my first year of graduate school. Three years later, I still feel that I am an average graduate student. However, I also feel that since I started graduate school I’ve gained a large amount of confidence and greatly developed my knowledge in geology, chemistry, and mathematics. I have also been humbled. Although I know much, much more than when I started graduate school, I have also more fully realized what an enormous amount of knowledge there is in the world and how much I don’t know. Most importantly, I’ve learned not to be afraid of a little scientific perspiration, be it picking crystals for hours on end, teaching myself an ancient data reduction program, or jumping headfirst into some math.

Carbonate grains under the microscope, Fall 2010.

“Genius is one percent inspiration and ninety-nine percent perspiration.”
-Thomas Edison

If you’re average but want to be a scientist, there’s hope! With persistence and a fair amount of perspiration, you can still become a great scientist.

Most of us are not scientific geniuses or autistic savants. Most of us are, well, fairly average. We should be. Most people are supposed to be average. Most of us should be C-level students. C is supposed to be average, the recent trend in grade inflation aside.

Take me, for instance. I may go to MIT and all that jazz, but really I’m quite ordinary. For instance, in the three math classes I’ve taken since high school, I’ve earned two Cs and a B. In many ways, I’m quite dumb by MIT standards. I suffer from math anxiety, like many people, and I have trouble memorizing information. I forget mineral formulas and phase diagrams. I’m slightly dyslexic and mix-up phrases and reverse numbers. I’m a klutz, though I’m more graceful than I used to be as a kid. Still, in the lab I have to work very carefully and constantly be aware of myself. I’m the sort of person to pick crystals for three days and then accidentally knock over the beaker onto the floor of the lab. I’ve done it before.

I am a fairly creative thinker and a decent writer, but in most other ways I’m about average. I hardly fall into the category of MIT genius. Like most people in the world, I don’t solve problems in fluid mechanics by gazing into my coffee cup (like Albert Einstein) or take up animal behavior studies by training the ants in my bedroom (like Richard Feynman). Unlike other MIT students, I don’t play competitive scrabble in my free time or whisk off to Vegas to win thousands by card-counting at Blackjack. I’m just a fairly average graduate student, my MIT credentials aside.

Still, there is hope for me as an average scientist. And there’s hope for you, too, if you’re also average like me! This hope comes from the fact that good science does not come exclusively from intellectual giants who come up with a great idea and immediately change the way we view the universe. We are not all Albert Einsteins, Richard Feynmans, or Carl Sagans. Even these great thinkers had to work fairly hard, long hours to come up with their strongest science. Sure, they were naturally talented in mathematics and their respective scientific fields, but that wasn’t enough. They also had to spend countless hours calculating, measuring, and writing. They not only had to come up with their ideas, they also had to figure out how to prove them and explain them to others.

As science grows more complex and interdisciplinary, the role of many hundreds of average scientists will be just as valuable as the role of one or two great thinkers. There are many problems science needs to tackle in this century and beyond, and we need as many minds as possible working on these problems. In order to be able to cure cancer and figure out issues such as climate change and sustainable energy, we need global scientific efforts.

I think a great misconception in the world is that one has to be really smart or naturally great at mathematics and science to be a good scientist. This is false, in my opinion. Sure, having some natural ability doesn’t hurt. More important, though, is having a real passion for science and being willing to work hard at science because of this passion.

When it comes down to it, science is often about persistence. Because science explores the unknown, there are no certainties. There’s a big difference between the textbook answers in a freshman college physics or chemistry lab and real scientific research. Scientific research is more often than not one step forward, ten steps back. Progress can be very slow and tedious. A great idea can take months to years to test and verify. Sometimes, smart people are not very good at hard work and persistence.

In my own life I’ve watched friends give up on science degrees when there were suddenly no textbook answers, when success required working through a little frustration. An ex-boyfriend of mine switched to finance after he realized biology was “a little more difficult” beyond the introductory level. He was smart enough to become a biologist, but he didn’t want to work hard for the answers that were not already there. The same semester he switched to finance, joined a fraternity, got drunk every night, and we broke up. He moved on to a pretty Asian girl, and I moved on to a research job in a geology lab. I like to think I chose science over him. It sounds more romantic than “he dumped me for a hot Asian chick.”

Personal stories aside, though, I feel that often the scientists who make the most valuable contributions to science are not the smartest ones but rather the most persistent ones (or perhaps the luckiest ones). These persistent scientists may not be geniuses in the Einstein sense, but they are willing to trudge away for years at a task that many might find extremely frustrating or boring. For instance, the Serbian geophysicist Milutin Milankovic was smart, but he did not become famous because of one moment of brilliance. Rather, he became famous because he devoted himself for thirty years to the tedious calculations associated with the planetary and solar system cycles that affect climate and ice ages. The Milankovic Cycles are controlled by Earth’s orbital shape, eccentricity, and axial tilt and are now recognized to play an important, natural role in climate regulation. The theory that physical variations in Earth’s movement may affect climate had been advanced before Milankovic. However, Milankovic was the first person to sit down and grind through the tedious calculations, so the cycles are named after him. He was willing to do the hard, often boring work that others were less willing to pursue. He worked hard.

Fortunately, modern technology is somewhat easing the amount of hard– or at least monotonous– work that scientists must do these days. Computer programs make repetitive calculations much more bearable and also much faster. Fancy equipment in the lab automates many of the more laborious aspects of chemistry, physics, biology, and engineering. Once one works his (or her!) way up the ranks somewhat in science, one can also hire graduate students, a cheap and often efficient way to complete less-than-desirable yet still important calculations or tasks in the lab.

Regardless, I think that dedication and hard work still count for a great amount in science these days. At least, that’s what I tell myself. I am not the hardest worker in my lab, by any means. I do often work long hours, though, and I try not to complain when the tasks are repetitive or frustrating.

For the last three days straight, I have been picking plagioclase crystals under a microscope. By picking I mean selecting crystals that are not altered significantly so that they are good “bottles” for the radioactive isotopes I am using to date the basalts from which these crystals came. These crystals are very small– they’re about 250 microns wide, on average. I use a very small pair of tweezers and pick in a dish filled with ethanol so that the crystals don’t stick to my tweezers as I’m picking them. I have been picking between eight and twelve hours a day with limited breaks. I go to the microscope, pick for a couple of hours, have a cup of tea, pick for another hour, eat lunch, pick for a few more hours, check email, pick for an hour, go to the gym, pick for two or three more hours, and then go home. By the end of the day, my right hand muscles ache and my eyes are sore. I walk home seeing tiny white plagioclase crystals dancing in front of me. While picking, I have listened to just about all the music I own and have started begging my friends for new mixes.

I’m exhausted, but I don’t mind my crystal picking too much. The task is monotonous, but it’s also very important. Picking crystals by hand is the best way to ensure that the dates I end up obtaining for the basalt rocks are the best dates possible. If I know the the crystals are good (unaltered, pure, clean plagioclase) then I can have confidence in my ages once I determine them three or four months from now. For a couple of unpleasant weeks of picking now, I’ll have a great scientific return in the future… hopefully, anyway. Nothing is guaranteed in science research, after all, but my chances for good data are high.

The work I’m doing now may not be as significant as, say, thirty years of Milankovic calculations. Regardless, as I sit here in my lab, at the microscope, picking away for hours on end, I feel somewhat romantic. Hey, I may not be the smartest scientist around. Here I am at MIT, though, and dammit I’m going to work hard.

So, that’s my message for today: a little enthusiasm and dedication can go a long way in science. Not the brightest but still want to be scientist? That’s okay. Work hard, and you can succeed in science. At least, I hope so. We certainly need more scientists in the world, so it shouldn’t be just the very top cream of the crop who pursue degrees and careers in science. We need some average, hard-working people to become scientists, too. And after all, even scientific geniuses have to work hard to provide concrete support for their far-fetched theories.

Brilliant Clutter

My home dining room table, cluttered with computer, papers, notebook, phone, and cat, Spring 2010.

Some of the most brilliant, productive people I know have the most cluttered offices and homes. For instance, I know of one MIT professor whose office is a mess, though he always knows where to find things. Similarly, my friend and mentor James Randi has an office that is full of clutter. Randi doesn’t know where to find things, generally, but his cluttered office doesn’t keep him from doing brilliant work.

Is there a link between clutter and brilliance? Are brilliant, productive people just less concerned with details of keeping house than with their work? Does the lack of time spent tidying up translate into more time for doing more interesting work?

Of course, I am generalizing. There are plenty of brilliant, productive people who keep their offices and homes immaculate. One could argue, just as easily perhaps, that there’s a link between obsessive compulsive disorder and brilliance. However, looking around the halls of MIT, I see clutter, mess, and brilliant work everywhere. Is the scientific mind, the mind of an engineer perhaps, prone to clutter? Or at least prone to not worry about clutter and keeping up appearances?

Personally, I fall somewhere in-between extreme clutter and extreme neatness. Growing up, my room was certainly a mess. I cluttered my room with rocks, books, and sporting equipment. I rarely dusted my bookshelves or made my bed. I shoved large quantities of artwork, shoes, books, and stuffed animals underneath my bed in my infrequent cleaning attempts. My parents rarely lectured me to clean my room, which was great. The forts I built out of sheets and pillows could stay up for weeks (along with the “No Boys or Little Sisters Allowed” signs), and I was free to organize and re-organize my rock collection, laying out various pieces all over my room. The time and freedom I gained by having a messy room far outweighed the benefits of keeping up appearances with a clean room, though I did have to tidy up whenever my grandmothers came to visit.

As I’ve grown up, I’ve become more tidy. I still have far too many rocks, books, and sports equipment items in my apartment, but now I make my bed most mornings and vacuum and dust on a regular basis. I find that I think and write better, often, in a somewhat neater space. Cleaning can also be relaxing, at times. Sometimes, I clean when I want to think about something but also want to feel productive.

However, I still allow myself to be somewhat cluttered, especially if I’m organizing something or working on an intense project. And if I end up becoming a working mom, my house is undoubtedly going to be somewhat cluttered. Why? I want my kids to have the freedom to live in their house without worrying about being perfectly clean. Also, I don’t want to feel that I need to keep things spotless when I have a big deadline at work or a distant volcanic expedition to plan. If my husband wants to clean up or hire a housekeeper, fine with me.

My desk is still a cluttered mess, most days, but that’s okay. After all, as Albert Einstein said, “If a cluttered desk signs a cluttered mind, of what, then, is an empty desk a sign?”

Besides, clutter is more fun. Who wants to clean up their desk or room, anyway?

*When I wrote this, I was still with my first advisor, whom I left at the end of my second year of grad school. I am now co-advised by two scientists. One of my advisors has a nearly spotless office while the other has a moderately messy office that is full to the brim with maps, books, papers, and so on. I’d argue that both of my advisors are brilliant scientists.

Caught in a Bad Project

A friend* just sent me a link to this video called “Bad Project,” a parody of the Lady Gaga song “Bad Romance.” I think this video is hilarious! I love the Lady Gaga outfits made out of laboratory supplies.

 Video taken from Youtube.

Since I am currently on my third PhD advisor (I left my first advisor, then my second advisor took a job at another institution- though to his credit he still advises me from a distance), I have had my own graduate school frustrations. Fortunately, I actually have a “good project” and am finally making headway and feeling optimistic about my research. 

However, like many grad students, I have had days where I am so frustrated with graduate school and academia that I daydream about fantasy alternate careers. After awhile, I remember that I really do love geology, and that– despite all the hard work and frustrations– I’m right where I want to be. I’m not yet sure if I’ll “make it” as a professor at a high-pressure research institution (nor if I want to pursue such a career), but I know that I love geology and want to be a geologist, whether it be through working for a company or teaching or research or some combination of the above. 

In moments of stress, grad school friends of mine talk about becoming musicians, artists, novelists, and businessmen. They daydream about opening surf schools, bakeries, and kumquat farms. I think many grad students have fantasy alternate careers that they will pursue “when this whole grad school thing doesn’t work out.”

My own fantasy alternate careers?
-Park ranger or game ranger
-Archaeologist
-Novelist
-Professional kayaker
-Translator
-Owner of an adventure tour company
-Professor of Middle Eastern Studies or Arabic
-Jane Goodall (yes, I want to be Jane Goodall)
-Running a cat rescue shelter (my cat-allergic fiance vetoes this one, though)

What are the fantasy jobs that help you survive graduate school?

*Thanks, Fern!

Bee-Bop the General Exam Bear

Bee-Bop on my desk after I passed my general exam, Woods Hole, October 2008.

This is Bee-Bop, the big, furry, creepy, blue toy that PhD students in the Geology & Geophysics Department at Woods Hole Oceanographic Institution (WHOI) pass from student to student. The toy is held in the possession of whomever has most recently passed her (or his, but most geology students right now are female, so I’ll go with her) general or qualifying exam for her PhD. When a new student passes her general exam, Bee-Bop appears on her desk within a few hours– usually when the newly-minted PhD candidate is busy drinking the important post-generals beer or taking the relaxing post-generals nap.

The Bee-Bop toy has been passed down for the past four-and-a-half years that I have been a student at WHOI. I don’t know when the tradition started. If any WHOI graduates read this and know when and how this tradition originated, please let me know. Bee-Bop resided in my office for about two months. I passed my general exam in early October of my third year of graduate school, and I handed over Bee-Bop to another successful PhD candidate in December of that year. I believe that Bee-Bop currently lives in my friend Arthur’s office. Depending on when students take their general exam, they have Bee-Bop for a few days or for a few months.

Most PhD programs have a notorious general or qualifying exam. Some programs even have two such exams! Prior to this exam, you are not, technically, in the PhD program. After this exam, you become an official PhD candidate. The exam varies from institution to institution and from department to department, but usually the exam consists of a general knowledge section, which can be written or oral, and a research section, which is often an oral presentation and accompanying research paper. The general exam is graded by the notorious general exam committee, which again varies from institution to institution. At some places the exam committee is selected by the department whereas at other places the student is allowed to select her exam committee. General exams usually happen at the end of the second year of the PhD.

In the Geology & Geophysics Department in the MIT/WHOI program, the general exam currently follows the guidelines below. Note that these are the guidelines that I followed and which I believe the department still follows but that this is a blog and does NOT represent the official MIT/WHOI rules on the matter.

1. The general exam committee consists of committee members (usually 2-4) selected by the student plus the student’s advisor(s) plus 1-2 committee members selected by the department to serve on all of the general exams in a particular year.

2.  The student must present two 20 minute presentations about two separate research projects. The student must also write two ~10 page research papers, one for each project. The committee members read the papers in advance and then listen to the two presentations. After each research presentation, the committee members can ask questions about the project.

3. After the research portion of the exam is concluded, the committee members are allowed to ask general knowledge questions. Committee members can ask anything they want, though the questions are often within fields (e.g. geophysics, geochemistry, sedimentology, paleoclimate) the student is supposed to be knowledgeable about for her thesis.

Most questions are reasonable, but the committee members will sometimes ask harder and harder questions until they find a question the student cannot answer. Then, they observe how well the student responds to a question she has absolutely no idea how to answer. There are all sorts of rumors about the worst general knowledge questions. Rumored worst questions ever are:

“If your airplane crashed and you were on a life raft in the middle of the Indian Ocean, what kind of science experiments would you conduct?” (To a physical oceanographer)

“What is the moon doing right now?”  (To a student studying lunar basalts)

“If the Earth were two-thirds its present size, how would all of geophysics change?”(To a geophysicist)

4. Because two research projects are required, the general exam happens in the third year, which is a little later than most PhD programs. Students do not take the exam at the same time. Rather, each student takes the exam when she is ready. Thus, general exams are staggered throughout the third year, which gives Bee-Bop time to reside in each student’s office.

5. The general exam varies in length but generally lasts about three hours. Scheduling two hours before lunch is recommended as your committee members become hungry and tend to ask fewer general knowledge questions.

The general exam is really scary and stressful. For about three or four months before my general exam, I was really stressed out. My exam was a little more stressful than most, I suppose, because I was in the process of changing advisors. However, all students (at least ones I’ve observed) stress about their general exam. In my program students who actually make it to their general exam almost always pass. Somehow, the knowledge that you are pretty much guaranteed to pass (at least in the Geology & Geophysics Department) does not make the general exam any less stressful.

Yes, most students pass their general exam here in the Geology & Geophysics Department at MIT/WHOI. This is mostly because advisors don’t let their students take the exam until they are ready. The students in the program are bright (being accepted to the program is the hard part, really), so they are generally quite capable. The students who don’t pass outright usually pass with some conditions. A conditional pass sounds scary, but usually it just means that your committee wants you to take an extra thermodynamics class or write an appendix to one of your general exam research papers. A conditional pass is not a bad thing; such a pass just means that your committee wants to make you a better scientist.

Rarely (in geology, but not in other departments such as engineering), students fail their general exams. There are two versions of this failure. Outright failure (leave the program immediately with nothing) is extremely rare. The second type of “failure” is the committee requiring that the student write and defend a masters thesis. After defending this masters thesis, the committee will then re-evaluate if the student is ready for a PhD. Some students who receive the “masters failure” become frustrated and decide to leave with the masters; others persist and continue with the PhD.

The MIT/WHOI program does not award masters degrees as a matter of course. You cannot apply to be a masters student (unless you are in the Navy, which has a special arrangement), so a silly notion about the MIT/WHOI program is that receiving a terminal masters degree is a “failure.” Clearly, this is a ridiculous notion since a masters degree from MIT/WHOI is considered extremely prestigious by PRETTY MUCH THE WHOLE WORLD. Only in the confining bubble of academia (and not even all of academia) is obtaining a masters degree from MIT/WHOI considered “failure.” Honestly, I don’t think anyone at MIT or WHOI really looks down upon anyone who decides to leave with a masters degree. Nonetheless, since the expectation when you start the program is that you will obtain a PhD, people sometimes whisper in hushed, gossipy tones about so-and-so defending her masters.

Sometimes, students decide to leave with a masters degree even before they take their general exams. There are a number of reasons for this, but most often (from what I’ve seen) a student realizes that she doesn’t want to be a PhD academic. These masters-choosing students leave the program and generally obtain excellent jobs, making their PhD-seeking former classmates extremely jealous of their money and free time.

The general exam is a rite of passage for all students in my program. As with many rites of passage, there are some traditions. Generally, there is cake and a small party and a free-pass from your advisor to sleep in for a week. In my department, we also have Bee-Bop.

I suppose that I should explain a little more about the Bee-Bop toy. I call this toy a bear, but really the toy is some kind of strange space alien mutant baby. I guess it makes me feel better to think about Bee-Bop as a blue bear with a strange head than a mutant alien baby with a blue bear body. Bee-Bop is a ridiculous and very creepy toy. Just looking at the toy is creepy enough. However, to make Bee-Bop even more creepy, this toy does not one but TWO creepy dances. Unfortunately, I did not videotape Bee-Bop’s dances when I had him (her? it?)  in my office. Fortunately, there are many videos of this toy on YouTube. I found several videos by googleing “creepy dancing toy.” Here is a video of an orange Bee-Bop that I like:

Video taken from YouTube.

As you can see, Bee-Bop’s name comes from the sound it makes when it starts its first creepy dance. When I found this video on YouTube, I realized that Bee-Bop’s name is actually Boohbah.  The toy is apparently based on the creepy children’s television show Boohbah, which started in 2003 (UK) and 2004 (US). Thus, I deduct that the Bee-Bop/Boohbah general exam tradition started around 2004.

The Bee-Bop toy is crazy and silly and creepy and always makes me laugh whenever I see it in a classmate’s office. Shortly after my own general exam, I made the Bee-Bop toy dance its creepy dances in my office. The Bee-Bop dances made me break out into hysterical laughter with my officemates. After I survived– and passed– my general exam, laughter was just what I needed.

I hope that the Bee-Bop toy continues to be passed down for many years. If the tradition is ever lost in years to come and some future graduate student in the MIT/WHOI program finds this blog post, please contact me. I volunteer to buy a Bee-Bop toy off ebay (if ebay still exists) and mail (maybe teleport– that would be neat) it to whomever has just passed her general exam.

Mystery Novels and Mass Spectrometers

The Element2 mass spectrometer at WHOI. Image taken from here.

This past week geoblogger Callan Bentley of Mountain Beltway reviewed books on time, fallacies, dirt, and climate change. There are some great books in his reviews– some I’ve read already and some I’ve added to my reading list. Alas, I am afraid that my reading list is quite long. I’m very impressed at how many non-fiction books Callan manages to find the time to read. I think Callan must be superhuman– he seems to do so much!

In recent years, I have found that my reading habits have changed somewhat. Since childhood, I have been in the habit of reading every night before bed. I still read most nights before bed, but I’m afraid that both the quantity and the “quality”, so to speak, of my reading has degraded since I started graduate school.

The degradation of quantity is easy to explain. I just don’t have as much time and energy for reading. As for the “quality” of my reading, I read far more “serious” books in high school and undergrad than I do now in graduate school. There are dozens of non-fiction books about geology on my reading list, but I find that I only read two or three of these books a year. Instead, I read science fiction, fantasy, and mystery novels. At least, this is what I read in my free time. I guess that if you count research for my thesis, I do read a fair amount of non-fiction geology in the form of papers, research books, and others students’ theses. I think all the reading I do for my PhD research leaves my brain somewhat tired. Much as I want to select (looking at my bookshelf) a book such as “Volcanoes of the Solar System” for my nightly reading, I am much more likely to pick up a fantasy or mystery novel.

In addition to being a bit burnt out from all my reading for my PhD, another reason I select somewhat lighter books these days is that much of the time I have for reading I also need to periodically be paying attention to other things– namely, chemical separation columns and mass spectrometers.

For example, on Wednesday I spent 10 hours measuring uranium and thorium concentrations on the Element2 Mass Spectrometer here at WHOI. 10 hours is actually a very short day for me on the Element2. Normally, when I run this mass spectrometer I run for 14-16 hours. There are two reasons for this. First, you pay about $1000 per day to use the machine, so you want to maximize this time. Second, it takes two or three hours to set-up and tune the machine. Once the machine is tuned, you want to run as many samples as you can.

When the Element2 is running poorly, I have to pay close attention to every sample and continually re-tune the machine. However, when the machine is running well– as it was on Wednesday– I have about three minutes of waiting time for every blank, standard, and sample I run. I still need to stay at the machine in case there is a problem (unfortunately my samples are too valuable for me to risk automating the analysis), but I don’t have to pay close attention.

I have tried doing various “productive” things during this waiting time such as reading journal articles, reducing data,  and writing parts of my thesis.  However, I have found that trying to be “productive” during the waiting time is futile. Three minutes isn’t enough time to focus and make progress, so I just end up re-reading the same sentence of a paper a dozen times. So, after the first two times I ran the mass spectrometer I gave up on trying to do “productive” activities during this waiting time. However, I found that just sitting there for those three minute stretches (for 12+ hours) is mind-numbingly boring. So, I have found that reading a book– the type of book that can easily be picked up and put down– is a good solution.

Certain types of science fiction, fantasy, and mystery books are perfect for this “pick up and put down” reading. Last year, I made my way through the Sword of Truth fantasy series, much of which I read while waiting for a column to drip or a mass spectrometer to analyze an isotope. Currently, I am making my way through the Elizabeth Peters Egyptian mystery novels. I anticipate that the Peters novels will carry me through the rest of my labwork this year.

The Sword of Truth fantasy series. Image from Wikipedia.
The first Elizabeth Peters Egyptian mystery novel. Image taken from here.

I plan to take a few months off after I finish my PhD before I start either a job or postdoc. This planned break gives me time to join my fiance abroad and go through immigration and such. Also, this break will give my brain some rest after many years of school. Hopefully, during these months off I will tackle a good portion of my reading list– and not just the rest of the Peters mysteries, delightful as they may be.