D-FENCE!

In basketball (and most other sports), defence wins championships.  A good “D” will give you the right to keep on playing.  In science, a good defence gives you the right to add three letters to the end of your name, the right to be called “Doctor”, and, also, the right to keep on playing.

Over the last month, I’ve taken a hiatus from blogging, and from pretty much everything else in my life (other than the occasional NBA playoff game), in an effort to prepare for my defence.  Like most PhD candidates, I have my thesis studying routine, which slowly turns into a thesis studying rut.

The flexible hours mean I wake up later and later each morning.  I try setting my alarm clock and giving myself study goals.  Unfortunately, this is countered by daytime TV.  For some reason, I can’t I help wondering if Regis is back from vacation.  Who’s on Ellen today?  What kind of party are they going to be throwing for Meredith now that she’s leaving The View?  Is there anything on TBS?  What’s Oprah about today?  Should I send money to The Angel Network?

Should I go to the library to study?  Like some lowly undergrad?

Forcing yourself to keep the TV off then results in “the hunger”.  Wouldn’t a snack be nice?  There’s popcorn, cereal, leftovers, cookies, chips...  You remember that many students have gained weight while studying for their defence, and that you haven’t worked out in a while, so you now have to go to the gym...

Then there’s the internet.  Anything new on PhD Comics?  What about Fark?  Waiterrant.net?  Now for the news and the science blogs....

Continue reading "D-FENCE!" »

News & Views: Update

Corresponding Author: J. Dee

Since around the Christmas break, Kev’s been “finishing up” his PhD.  He’s pretty much stopped bench work, wrote (and submitted) several papers for publication, drafted a grant proposal, and most recently, began writing his thesis.  Kev’s been busy lately, and understandably, hasn’t had much time to blog.   Since it looks like things won’t be quieting down in the immediate future, I’m attempting to temporarily to fill the void. 

This is a pretty exciting time.   The post-doctoral search ended not too long ago, and was an unbelievable success (no details yet – I’ll let Kev break the news!).  After 5 years, the end of graduate student life is in sight! 

I don’t know how different things will be once Kev graduates from “grad student” to “post-doc” (I expect it’s kind of the same thing, but with a little more money and a lot more responsibility - correct me if I’m wrong).   We’re currently in the middle of that transition, with Kev working most days at home.   Because he’s mostly here now instead of at the lab, I have something to look forward to at the end of the day.   So that’s one immediate benefit of Kev “finishing up”.

And there’s a whole bunch more in store –  moving to another big city and to another state, applying for work visas and new drivers licenses, finding a new pad, enjoying unemployment (attorneys must to re-license when changing jurisdictions – a 3-month process), letting Kev assume the role of “breadwinner” for a little while, and best of all, warmer climates!

It’s taken a long time to get to this point and it’s exciting to be here. 

The Postdoctoral Search: California Love

Hr10003684037 “I asked Jonas Salk why he came here and he said the weather.... I asked Francis Crick why he came here and he said the weather” (Joe Panetta, quoted in San Diego: California Dreaming by Paul Smaglik. Nature 422, 240-241, 13 March 2003)

Looking out the airplane window, I finally see southern California.  The sun is shining bright yellow, and tropical palm trees are everywhere.  There are fields of lush, green, grass, and every-other house has a whirlpool or swimming pool behind it.  There aren’t any skyscrapers, which is usually a concern for a city boy.  However, the landscape is so beautiful and unique that all you can think about is the word “vacation”.

About a month ago, I had a phone interview with one of the world’s top scientists.  I would have had absolutely no chance to get into this lab, but my supervisor pulled some strings with a colleague (who was this famous scientist’s previous postdoc), and got me an interview.  The phone interview was quite long (about 1.5 h), with questions starting from my high school education (YES, high school! Over 8 years ago!) and ending with discussions about the current state of our research.  Now, I am not the type to get nervous – I don’t mind interviews, public speaking, being put on the spot, etc.  This phone interview, however, had me so nervous that I couldn’t remember what happened until the next day.  Apparently, he subsequently set up phone meetings with my supervisor and his ex-postdoc, and they talked for some time about my abilities.  Finally, I was granted the opportunity to visit his lab.

California is quite a different place.  People are tall, healthy, thin, and beautiful.  In Boston, “How do you work in this weather?” meant “How do you work in the blistering heat without air-conditioning?” or “How do you get to work in this snowstorm?”  In California, it meant “How do you work when 300 days out of the year are warm and sunny?” 

Just the trip to California was amazing – we crossed the Grand Canyon!  Then, on the way to the hotel, my aunt (who is a Californian) drove me to see a few celebrity houses.  Tomorrow, I would explore the Salk Institute and try to spot (and maybe even get a picture with) a “real” celebrity – Sydney Brenner.

For those not in the field: Sydney Brenner was previously known as “the perennial Nobel Prize bridesmaid” until he finally received it with Robert Horvitz and John Sulston in 2002 “for their discoveries concerning ‘genetic regulation of organ development and programmed cell death’”.  Previously, he discovered messenger RNA, and, with Francis Crick, discovered the triplet code of protein translation and frameshift mutations.  His work with C. elegans provided insights into aging, cell death, and nerve cell function.  He is now studying gene and genome evolution, and has revealed new ways of analyzing gene sequences.

The Postdoctoral Search: The Cambridge Experience

Harvard_2   

Harvard is bustling with activity.  It is the prototypical, traditional, picturesque, Ivey-league school.  Beautiful historic buildings surround small grass fields and water fountains.  Tiny trails, lined with park benches and flowers, lead all over campus.  Tour guides are leading around groups of shy, prospective students, each surrounded by their slightly-more-than apprehensive parents.  J.D. and I follow a tour for a little while.

“Can you live in residence for all 4 years?” a mommy asks the tour guide.

“Yes, people tend not to, but yo-”

“You hear that, honey? You can live here all 4 years!” mother hen speaks to her daughter like she’s 6-years-old.

“What about the food plan? Can you get that all 4 years too?” asks another.

“Y-You could, bu-”

“That’s great!” yet another parent interrupts.

The students don’t ask a single question.

J.D. and I look at each other.  Were we ever this young? 

We leave the tour and head towards the cafeteria for a bite.  We sit next to a couple of Harvard undergrads.  They spend the lunch discussing Jessica Simpson and the Dukes of Hazzard.  J.D. and I whisper to each other, “Are these students really that much smarter than we were?”

A bit later, J.D. leaves to go do her exam, while I head towards the labs.  I’m lucky enough to have interviews with several of the biggest labs on the main campus, although I don’t have any at the Dana-Farber Cancer Institute in Longwood.  Entering one of the buildings, I notice in the building directory that pretty much the whole building is devoted to one of my potential bosses. 

Many new Universities are paying big bucks to renovate their buildings, keeping a traditional exterior, but with a highly modern interior.  This building, however, is old on the outside and old on the inside.  There is no air-conditioning, which is a severe problem for many chemistry labs.  Many chemicals begin to evaporate in warmer weather, and I can smell some of them here. 

In the lab, the students have moved many of the evaporating chemicals into the fume hoods.  Everybody in the lab is sweating because of the heat.  I ask how they work in this weather.  “You get used to it,” a postdoc shrugs.  The lab rooms are old, with old, creaky, hardwood floors, wooden benches and wooden cupboards.  There’s old equipment everywhere.  Chemicals line the hallways, in old, rusted drums.  Like many labs, they’ve framed and hung all the journal cover-art that they have published.  The interview is nice, as are all the lab members.  I go through my list of questions, asking specifics about their supervisor, the work environment, ex-postdocs, etc.  The whole process is harmless, but the heat has gotten to everybody.  We all speak slowly and sluggishly.

Outside of the building, I notice an honorary plaque stating that “Charles Dickens was here”.  I guess this building was state-of-the-art when he was here, but it’s 2006 now.

At the end of my lab interviews and tours, I notice the same theme.  On the main campus, the big supervisors are typically in the old buildings with the old equipment.  Nothing impressive, in terms of state-of-the-art equipment and facilities, really jumps out at you.  Many don’t have more funding (at least per person) than a typical lab, but they do better because they are smart, and work smarter.  Most importantly, supervisors have extremely smart people working for them.  They have an advantage in that they have an extremely smart pool of undergrads to draft into grad school.  As usual, labs are understaffed and postdocs work about 70 h a week (these two points are not related).  All-in-all, the labs are very typical.  It’s just the intellectual work – the published papers – that stand out from your average lab. 

One principle investigator offers to pay for my plane tickets, but I decline.  Cambridge and Boston are nice, but I don’t think they're for me.  There is no metropolitan feel, and the multiculturalism is pretty poor (although since I’m from Toronto, I may be asking for too much).  J.D. was miserable, and for us, the city wasn’t “fun”.  Harvard is Harvard, and I would have loved this place in undergrad... but I guess I’m older now, and looking for a “special” postdoc – big lab, interesting work, fun people, a beautiful city for the rare hours a postdoc gets to relax.... someplace with that certain je ne sais quoi (air-conditioning!?!).  Anyways, I didn’t want to let the potential boss know that I’m not flying back home.  I’m off to tour the West-coast labs... California!

Next Up: California Love

The Postdoctoral Search: Boston

Late last summer, the search for a postdoctoral position took me to Cambridge.  Knowing that we would eventually be moving to the States, my girlfriend decided to schedule her American legal ethics licensing exam at the Harvard campus so that she could write them while I did my interviews.  As the days led up to the trip, I noticed that everybody kept on saying, “Boston is a really old city.”

“What do you mean?” I would ask.

“It’s... just... it’s really old.”

Throughout the plane ride, I would daydream about being asked,

“Where are you going to do your postdoc?” or “Where do you work/go to school?”

“In Boston,” I would reply.

“Boston University? Boston College?”

“Uh... actually Cambridge,” I would clarify

“Where?”

“Harvard” – I was beaming inside.

As a graduate student, your family and friends typically have no idea what you are actually doing for a living.  They wonder why you didn’t go to med school to become a “real” doctor.  If I could tell them I’m working at Harvard.... well.... and of course, women everywhere would automatically assume that I was smart and/or rich... The shallow part of me was living it up.

After arriving in Boston, we stepped out of the airport into sweltering heat.  It was humid and hot, and heat waves could be seen behind a road jammed with cars.  J.D. and I hopped on a shuttle for the hotel.  After checking in, we decided to explore the city.  The city was old.  The streets were old, many of them set with brick, and many peppered with pot-holes.  The stores and shops were old, with fans but no air-conditioning.  There was a certain stench in the air, kind of like Philadelphia (another “old” city) on a hot summer’s day.

The city wasn’t multicultural, but at least the Boston accents were charming.  There was a noticeable colonial theme, with many small markets and historic buildings.  We went to Faneuill Hall Market Place, which was a local tourist attraction.  J.D. asked a cop for directions and he laughed at the fact that the woman was taking charge.  In general, the people seemed to be quite conservative.  Even on what the hotel concierge told us was the city’s posh-est street, people were conservatively dressed.  Nothing like Rodeo Drive or Park Avenue.  Could this really be one of the intellectual capitals of the world?  Home of the liberal Harvard, and the high-tech MIT?

After a few days in the city, the heat became unbearable.  It was 2006!  How could people live without air-conditioning?  And in such a densely packed city?  J.D. broke out into hives.  We had to take the subway to the Harvard campus, which made things worse.  The subway was densely packed with people and was several degrees hotter.  It was extremely dark, old (of course), and like every other subway, smelly.  It was like a sauna.  At the Harvard stop, we got off the train and headed for the stairs to go up to ground-level.  We were fighting the crowd, the darkness, the heat, and the toll the trip took – we were simply exhausted.  All of a sudden, the sun came bursting out at the top of the stairs.  Then a cool breeze hit us.  Welcome to Harvard!

Next Up: The Cambridge Experience.

Research Highlights: DNA Faces

440283af12_1Corresponding Author: Fark.com

Having cured all genetic diseases, scientists create 50 billion smiley faces using DNA (with pic goodness). Link

Smith, LM. Nature 440, 283-284 (2006)
Rothemund, PWK. Nature 440, 297–302 (2006)

Brief Communications: Anatomy of a Journal Rejection

What The E-Mail Says:

RE: NAT-84-2849
Dear Dr. X,

Thank you for submitting this manuscript to our journal. Papers accepted for publication must meet stringent requirements of high scientific quality and significance, originality, and priority. Unfortunately, the concept and technique of the work does not add sufficiently to the literature to warrant peer review.

We would like to suggest that this study would be more appropriate for another journal. This decision simply reflects the scope of our journal and the intense pressure for space, and we are compelled to make a preliminary selection of manuscripts at the stage of submission before peer review. 
Sincerely,

John Smith, Ph.D.
Editor

What the E-mail Means:

Re: PFO
Dear Dr. X,

Thank you for adding to the spam we get at our journal. We are telling you that you paper does not meet the stringent requirements of high scientific quality and significance, originality, and priority. However, the concept and technique of your work will be published in another paper next month (in this very journal). The senior author of that paper is a famous scientist. You can see why we won't let your paper go to peer review.

Send it somewhere else.  This decision simply reflect the way science operates.

Sincerely,

John Smith, P.ermanent h.eart D.amage
Editor

Figures and Tables: Who's The Scientist?

Picture2_1Drawings and descriptions of scientists by 7th graders before and after a visit to Fermilab are funny, yet depressing.  Marissa offers the most accurate description: "A scientist is hardworking, studious, detail-oriented, observant, intelligent, exacting, and patient. When I think of a scientist, I think of someone who sets out to find the facts without predetermining what the outcome is. During this process a scientist must be fair, honest and unbiased. A scientist must be exact by following all directions and recording every step and observation, so that the experiment can be reduplicated. He/she must check and double-check all of his/her work. A scientist is very important in our lives because all of the experiments he/she does in the lab can affect our health, environment, nutrition, and other aspects of our daily and future life." (Pictures and Descriptions)

Figures and Tables: Valentine's Day

Corresponding Author: Ren

Paperheartcutout_2

References:

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The Big Prize: Doctors of the Decade

Actors have the Oscar, and life scientists have Thomson Scientific's Doctors of the Decade.  Congratulations to everybody who made the 1995-2005 list!  Drs. Meir J. Stampfer, Robert M. Califf, Bert Vogelstein, and John C. Reed are #1 in the Clinical Medicine/Epidemiology, Cardiology, Oncology, and General Biomedicine categories, respectively.  Harvard, Johns Hopkins, and the Howard Hughes Medical Institute made strong showings.  Doctors of the Decade Lists