Thursday, April 30, 2009

This made my morning.

Well, that and the fact that I get to see the Dalai Lama speak today (fingers crossed picking up my ticket goes smoothly!)

Anywho---I'd like to introduce you to Movits. They're a Swedish group, and I guess I would characterize them as the best bastardization of swing and rap I have ever seen. Well...the only swing/rap I have ever seen. And it's in Swedish!

Wednesday, April 29, 2009

warning: craisin ahead!

A friend sent it to me a few weeks ago, and I've been pondering it ever since. Still thinking, in fact. And I think that these will continue to be something to return to as I finish up with classes and such over the next month.

Advice for Graduate Students: The 10 Suggestions for a Basic Research Career

by Mark B. Kristal, Professor of Psychology, University at Buffalo

1. Establish an independent line of research as early in your career as possible. If you can, do so even as a graduate student. Avoid the graduate student’s trap of thinking up experiments in other researchers’ programs that the other researcher has missed. Of course these are useful studies, but do not form the basis of one’s own independent line of research.

2. Be problem-oriented, not technique-oriented. Use a variety of techniques, methods, and orientations -- whichever are necessary to solve the problems at hand. Philip Teitelbaum used to recommend, back in the days of relay racks and electromechanical programming equipment that would take months to assemble for a single experiment, that whenever a study was completed, the equipment for the study should be dismantled, lest the experimenter be seduced into running another study with that equipment just because it was there. It is also painful to hear a major professor introduce one of his or her graduate students as “Jenny Green...she does c-fos” or “Tom Smith...he does meta-analysis”. This may interest potential postdoctoral sponsors who are looking to hire new Ph.D.s because of the skills they can bring to the postdoctoral sponsor’s lab, but this puts the new Ph.D. squarely into the role, perhaps forever, of technician rather than scientist. Remember, technology comes and goes, but the underlying questions are the meat of research. It is depressing to go to poster sessions at the big conferences year after year and see the same questions being asked over and over with different, more “cutting edge” techniques, presented by people enamored of the techniques rather than the research problems. If technology is so costly, in terms of equipment, learning time, and other resources, how does one avoid the trap of becoming technique oriented? The answer: collaborate.

3. Think beyond the next publication, or even the next grant proposal. Take the long view; look at the big picture. In other words, bite off a piece of question that may take a decade, or even a career to answer. There is a major difference between the scientist that wonders how to break the question into appropriate sized grant proposals, and one who wonders how to expand the question into a grant proposal. Furthermore, commit yourself to your question; given the time and energy it takes to answer an appropriate sized research question, pursuing a series of unrelated research questions in parallel rather than in series is often a sign of dilettantism.

4. If you do basic research, keep your eyes open for applications of your findings. On the other hand, if you find yourself doing applied research, keep your eyes on underlying theoretical implications. Often, the distinction between basic and applied research is arbitrary or fluid.

5. When conducting experiments, don’t accept answers or results simply because they are publishable. Keep plugging away at the problem until the answers or results make sense or satisfy you in terms of an overall schema. Most importantly, don’t accept other scientists’ answers; reputation is not a guarantee against being wrong.

6. Expect unexpected results. A great deal of research data is discarded because an experiment “didn’t work”. However, a well designed experiment should provide positive information regardless of how it comes out. Design experiments so that all outcomes yield something: a “no difference” finding is not the same as a “negative results” finding.

7. Don’t expect answers; expect more questions. Daniel Lehrman used to tell us that a good experiment will raise more questions than it answers. Perhaps non-scientists find this aspect of science strangely frustrating. However, the lack of a final solution distinguishes the scientist’s quest from the engineer’s.

8. Never stop asking questions. Questions are the stock-in-trade of the scientist. The corollary of this suggestion is “never make assumptions.” Of course, assumptions are a necessary part of hypothesis construction, but on an everyday practical level, and in terms of research design, assumptions can be disastrous. Many times I’ve located hiding escaped rats that my students couldn’t find because unlike my students, I did not assume that a rat could not “go there” or “do that”.

9. Choose a problem that excites you. It should excite you so much that you can’t sleep. It should excite you so much that when someone asks you the time, you blurt out your research topic.

10. Strive for elegance in research. The elegance of an experiment is in the quality of the thinking and the cleverness of the approach to answering the research question, not in the complexity of the design or the sophistication of the methods. Often, the most elegant experiments are simple, low-tech attacks at the heart of the problem. Study classic research in your field and appreciate the logic and thought that went into it. All too often students nowadays ignore older research because it isn’t available online, or dismiss it for using old-fashioned techniques. There is much wisdom and cleverness in some of those old papers. Reading them, learning from them, and citing them, is real scholarship.

© 2005, The International Behavioral Neuroscience Society

see original site here

After reading about a zillion papers, and also sitting through a discussion about a scientist who basically didn't follow a published protocol, and then wrote a paper claiming the protocol didn't work, I have some questions to think about:

-It seems like there are two choices: fast high throughput science that publishes un-validated data, or slower methodical science that publishes validated and carefully tested hypotheses. Why can't you have the best of both worlds? People are publishing these papers in Nature about huge phosphoproteome database analysis and make some pithy comments about it...and others publish papers elucidating the ACTUAL biology behind some of these "throw-away" the Journal of Biochemistry (a lower impact factor journal). Um. Really? "Cool" technology or "cool" problems should not automatically get the green light. Thoughtful and well-tested science should be the focus.

-The way we publish papers is awful. It doesn't make sense. End of story. (there will be more on this later---after reading about 200 papers so far this year, I have some real issues with science)

-Mass spectrometry = hard.

surprise easter egg to those who made it through! my top ten favorite songs (right now at least):
1. Oren Lavie's "Morning Elegance"
2. Magnet's "Lonely No More"
3. Regina Spektor's "Fidelity"
4. Värttinä's "Illmatar"
5. School of Rock's "School of Rock"
6. Thomas Newman's Theme to "Little Women"
7. Atmosphere's acoustic version of "Always Coming Back Home to You"
8. Ben Fold's acoustic version of "Effington"
9. Peter Gabriel's "Down to Earth"
10. The Bird and the Bee's "Polite Dance Song"

Tuesday, April 28, 2009

Grad Gala

...I love getting dressed up. In vintage dresses. And dancing. Oh how I love dancing...

Quote from my grandmother: "Bridget, look at your wrists! You really need some bling. Don't you have any bracelets?"

---being the lucky girl I am, my mom picked up four amazing rhinestone bracelets a few years ago at the estate sale of a family friend. Too bad they were at home. However - they are now back with me in Boston, so they just may make an appearance at a future gala.

But for now---I'll just remember this ball with fondness as I procrastinate writing a grant review for 20.400. Because I love me some learning!

Sunday, April 26, 2009

all sorts of updates!

...or when you realize holy cow! I have so much to say!

--I talked with the McCormick house manager on Friday, and it looks like I will be moving in the first week of August--they're repainting the whole place (woo-hoo!) and I might be able to get a bed! Well, more like two twin beds smushed together, but I'm cool with that, too. I have my first official event to attend on May 2nd (make-your-own pizza party!) and a barbecue on May 9th...both should be a rocking good time. This also means that I am now combing Craigslist like crazy to find furniture to buy and refinish/clean/whatever it needs. And no worries--I promise to bring a strong not-female person with me to all Craigslist locations. Camp Fire Girl's honor.

--Update on Harold Fairchild - another Boston resident looking up information on this gentleman came across my blog and wanted to donate two books he found that belonged to Harold...he found them at the same event I found mine. They're steam tables - basically lots of values in lots of columns and rows. For 100 pages. Gotta love the days before calculators... I still have not heard back from the MIT archives, and queries to EAA, FAA, and Pratt/Whitney have not been fruitful (they all suggested looking into the National Archives, which my contact in Pelham is doing). I was also invited to a special ceremony for the opening of the new library in Pelham as a perfect time to donate these books - it's in June after quals, so I'll probably make a weekend of the experience.

--It has recently come to my attention that my blog doesn't really have a "focus." I've thought long and hard about why and if I care, and my realization is that my blog is a reflection of me, and it is who I am. I'm a biologist, a big sister, a fond wearer of dresses, a student, a baker, a musician...I am not just one thing, and I am more than okay with that. In fact, I would have it no other way. I love that my life vacillates between Shostakovitch symphonies, internal ribosome entry sites, figuring out yet another way to make quinoa taste delicious, and overcoming/enjoying my addiction to vintage dishes. What I write here reflects this...and you can read whatever you'd like. It's like a friend serving you this amazingly delicious pizza--let's say the chicken, gorgonzola, spinach, mashed potatoes, and spinach pizza from Emma's---and you just decide you don't like the craisins. So you pick them off. Problem solved. If you don't really care about my rants about science...don't read them. I'm not going to hold you hostage and/or force feed you craisins. Promise. (although they are so. good. ever eat them with a spoon of peanut butter? = heaven on earth).

-the farmer's market opens June 6th! I cannot wait. It has been on my calender since June. Other projects include trying to find a place to buy my milk, cream, butter, and perhaps even cheese from a local supplier. (Boston people - any ideas?)

-a friend here at MIT has agreed to help me learn how to swim! I did swimming lessons when I was younger and got through everything but lifeguarding, but I don't know how to do the perfect form adult swimming exercise that would be ever-so-lovely for this bad knee of mine. And the last time I tried I knocked my head into the wall several times as well as kicking people in other lanes...the perils of being blind and without glasses. I found a pair of prescription glasses online, and I'm so excited to get them in the mail and try them out! Anyway - my friend was a varsity swimmer from Cal Tech. And probably one of the kindest guys I know. I lucked out. (now, to build up to seeing myself in a swimsuit again).

Wednesday, April 22, 2009

Monday in the City

It's Patriot's Day!

...also known as "let's shut down the city and let it be taken over by crazy people that think it's a cool idea to run 26 miles! at once! what nutters!"

...also known as the Boston Marathon. Phew. It was quite a sight. I went to see this guy after he finished putting his final engineering-optimization-touch on preparing food for the starving runners:

Isn't that yellow jacket just fantastic? All the runners were jealous...

Sunday, April 12, 2009

Happy Easter! (or, Happy Zombie Jesus Day! ...thanks Flarnie)

Enjoy your eggs, gigantic bunny, and scones/quiche today, friends! I'll be hiding eggs for my little brother next weekend while I am home, and I am already cooking up some positively GENIUS places to hide them. Watch out, J. You + me = GAME ON.

(also--my hair still looks like this sometimes. look for me when it rains. and you'll see the most fro-ed out head of hair you've ever seen on someone over the age of four).

Sunday, April 5, 2009

Exciting news!

I found out this past Friday that I'm going to be a GRT (Graduate Residence Tutor) for the upcoming academic year! I'll be living in a one-bedroom apartment in McCormick Hall.

It's a short walk to Kresage (where I have rehearsals for the MIT Symphony Orchestra) and the rest of campus. It is on Memorial Drive overlooking the river, and while my apartment won't have a river view, the penthouse certainly does:

Downtown Boston (the bridge is the Massachusetts Avenue Brige, and you can just barely see the sailboats coming from the MIT Boathouse)

It's obviously hard to see it now, but the slightly obtruse thing on the right is the Citgo Sign (near Fenway).

Fenway is in the center-ish of the picture.

You can kind of see the other tower in this picture (as well as the flower boxes! Apparently they have sat vacant for years, except for a box of wild chives that haven't been tended in a long time...I'm going to see if I can get some money to start an herb garden up there..mmm...)

There is a 360º walkaround on both penthouses (McCormick has two towers) as well as a lounge and kitchen in the central portion of each penthouse.

Anywho, McCormick is named after the deceased husband of MIT Graduate in biology 1904 Katharine Dexter McCormick.
I can't get over how cool she is...born in 1875, she grew up as a wealthy socialite, and after her father and brother died in her teens (from a heart attack and spinal meningitis, respectively), she decided to study biology at MIT. She spent several years learning all of the prerequisites, finally entering MIT in 1899. She graduated in 1904, butting heads with the administration, who finally allowed women to stop wearing hats in lab (feathers are flammable, you know!). She married Stanley McCormick after she graduated (obviously, at her family's Swiss chateau). However, he succombed to schizophrenia and was hospitalized/institutionalized the rest of his life until he died in 1947. This lead Katharine to champion for better health care for those with mental illnesses, and she donated quite a lot of money to that cause over her lifetime. She was also a suffragette (as was her mother), and upon hearing a lecture by Margaret Sanger of the prospects of a female method of birth control, devoted much of her time to funding the development of the birth control pill, which was approved by the FDA in 1960.

Near the end of her life, she was still unhappy with the male:female ratio at MIT, and the inadequacy of housing for female students made her last effort fronting the cost of building an all-girls dormitory (30 million dollars in do the math).

"I believe, if we can get them properly housed, the best scientific education in our country will be open to them permanently. Then I can rest in peace."

She died three years later, and donated her entire estate to MIT (I believe the largest single donation in MIT's entire history....fairly impressive!).

I'm really excited to be living in a place that is associated with such a woman. I feel lucky to live in a building under the influence of such an amazing invisible cheerleader.

I'm not sure when I'm moving in, but my official duties begin August 16th...plenty of time to think of all sorts of fun things to do with my girls. (I have girls! how cool is that?)

Saturday, April 4, 2009

Spring Fever

To echo Black*Eiffel:

"It's spring fever. That is what the name of it is. And when you've got it, you want - oh, you don't quite know what it is you do want, but it just fairly makes your heart ache, you want it so!" -- Mark Twain

Friday, April 3, 2009

it was really cool to overload the Broad's servers, until it ended up that all my hard work meant absolutely nothing.

Some of you might have heard me excitedly smile today that I have overloaded the Broad's servers... (before I go on, it's pronounced Brode rhymes with road - I can't have you all thinking it's Brawd rhymes with cod, otherwise you'll make mistakes I have already made quite enough thankyouverymuch). It was a feat I considered pretty impressive (my brother told me I should put it on my resume) ---that is until I realize it meant that I had spent hours and hours and hours on this project for nothing.

I'm doing a grant proposal right now for a class which is analyzing microarray datasets (we're talking 22,000 partions of data corresponding to the entire genome). My goal is to find specific genes that are upregulated and downregulated when a specific drug stimulates cells using hierarchcial clustering (I don't get how it works, really. That's why computers do it). If you know a specific genetic footpring cause by a drug, you can sometimes figure out how the drug is actually working, or a better idea of other drugs that are similar to it for novel drug targets for your disease/condition of choice. I'm working on Hyper IgE, a confounding/odd/mostly unstudied disease where your body produces too many IgE molecules (IgE is a type of immunologlobulin: it's a specific antibody that works inside your body to deal with infection; it's now best known for being involved in allergic reactions). So this is cool...and it's interesting to me.

But there is a problem. These datasets are enormous. Huge. Gargantuan. I had to download all of these signatures from one website, convert them all into a different file type, and then run them through an online program run by the Broad. I was having all sorts of trouble until I finally broke down and emailed their support staff, a guy named Peter (yup--first name basis now). He said that my datasets were just too large for the main server, so he set me up in the queue for the larger memory servers (which will allow my data set to run, but since so many people use them and they are in such high demand, the samples will take a long time to run). I also found a bug in their viewing program, which took them quite awhile to fix. Ultimately (21 emails later), I was told that all the data sets I had were confirmed incomplete (the server simply gave up). Which means I am at square one.

I cannot tell you how frustrating it is to tell a professor that you have worked really hard...but you have nothing. It's so sad...I just turned in my preliminary data, and it contains a table that is all filled up...except for these awful white cells that pretty much scream FAIL. Sure, my specific aims are lovely, and I have a nice chart about the drugs I'm looking into, but the actual meat of the proposal is simply missing.

I realize I didn't start soon enough. I realize I know little to nothing about computational work. I realize my poor five year old computer is about to 'splode from all of this abuse. I realize that I should have expected more problems initially and contacted the Broad immediately. I realize that even though I have spent every waking moment in the past week on the project, I have absolutely nothing to show for it.

But I also realize that I have been working so hard this semester. Trying to juggle lab and classes is driving me nearly batty. I am always always ALWAYS behind in something. And for someone that is happy to breathe a sigh of relief at the end of a day feeling on top of things, this is just not okay for me. Sure, people tell me "it'll be over'll be fine." Sure, I'll be "fine." ...if your version of fine means that I'm operating in a completely unsustainable fasion and inch away from just giving up because there is simply not enough time to do everything.

I am so behind. And glad that I wear exclusively glasses these days--because my eyes betray how much sleep I am getting. (although you can't miss the slight hunchback from all of this computer work). Excuse me while I go and drown my sorrows in dirty dishes and chocolate.

Update: it's a new day (thanks mom!). And it's going to start with Bollywood. So there, life. Take that!

(from Kal Ho Naa Ho - sorry about the bad quality, but it's a great cover...)

Wednesday, April 1, 2009

Eric Carle

This year is the 40th anniversary of Eric Carle's The Very Hungry Caterpillar" -- and in the vein of things that made a difference in my life, books were one of them. I was a voracious reader as a little girl, and his were my favorite to read - such cool pictures and silly fun stories!

Things have changed, with my reading material now titled "The genetic advantage hypothesis in cystic fibrosis heterozygotes: a murine study" or "Tumor morphology and phenotypic evolution driven by selective pressure from the microenvironment." No wonder I buy things like "Are You There God It's Me Margaret" from the thrift store to read (and help me decompress).

For more about Eric Carle, visit his website.

And now, I'm off to daydream about glue and tissue paper and brown bears while I futz around with data processing and some nonsensical clustering analyses. Because that's what I do.