On Saturday I got an email from my pal Kevin O'Connell, the first person I met when I went to grad school in Madison, that one of our other grad school friends was seriously ill.  Congestive heart failure and liver failure (after a life time of health problems).  She was down in South Carolina (she now teaches at the College of Charleston), and we are in Boston.  So we gathered some stuff together and jumped in the car to drive down there to see her - a 15 hours drive, but driving was the only possible way to get down there in time.  We dropped the dogs off at doggy daycare on the way and drove through the night.

We didn't make it.  We got as far as DC when I heard from one of my other grad school friends, Janice Flory, that she'd passed away during the night, at around 3:30 am. 

Damn.  I wanted to see her, to say goodbye.  She was my grad school buddy.  We were in the same lab, Marcin Filutowicz's lab at University of Wisconsin-Madison for five or six years.  Often we would work until 11 or 12 at night.  We'd be the only two people in the whole building.  It was at Madison that I came into my own, and did a lot of growing up, and Steph, who was in the class a year before mine, had a small part in that.  She already seemed like a full-fledged "adult" (in the good meaning of the term), what with a neatly kept apartment and a nice car (a Lexus, iirc, with a chrome plated piece that fit over the butt end of the muffler so it lent some class to the bottom of the back end of the car, and she was very upset that when she had the muffler replaced, they threw that away instead of putting it back on the car like she'd asked them to).  We drove that car - she trusted me to drive it - on a couple of major trips from Madison all the way up to the Upper Peninsula to visit her parents.  Just drive and drive and drive and turn when you get to the farm equipment.  I remember Dona York, another grad student in our lab, told me that she'd taken a similar trip with Steph up to the UP, and after hours of driving, moments before they pulled into the driveway, Steph said, oh by the way, I should tell you that I had a brother.  He's dead now.  And she hopped out of the car and greeted her parents.  Dona was like, what?  What?!?  So when I made the trip, I was psychologically prepared.  Steph did have a brother who died in high school, and her parents kept his room exactly as it had been when he was alive.  And her mom talked about his non-stop, as if he were still alive.

I apologize if I'm rambling.  I'm still sorting through my emotions.  Steph was my friend, my buddy.  And I feel bad because I'd lost track of her over the years, even though we were so close at Madison.  And when I think of her now, it's just sort of random memories that come to me now, shards and fragments of thought, without any particular order. 

Like (which is a word she taught me not to say over and over): Election night 1992, when we were at a Bruce Springsteen concert.  And when I took a bathroom break, the TV screens in the restroom showed me that Clinton had won - Steph was a Republican, and she tried to convince us all of the wonders of that philosophy (though our fellow grad student Russ Karls said, I don't have enough money to be a Republican).  I think she got it from her parents.  I asked her dad, Nat, how he felt when JFK was shot.  His response was: It's about time.  Wow.  But, well, some people thought that and apparently still do.  Steph wasn't that extreme, but she was disappointed at the concert when I came back from the bathroom to tell her that her guy had lost - and doubly disappointed a few minutes later when Bruce Springsteen himself announced, "Looks like we got ourselves a new President - Bill Clinton!" and half the audience cheered, followed immediately by the other half booing.  She said to me, I wanted Bruce to tell me!  Hearing the news from him would have softened the blow.

Brianna asked me during a break in our long drive what I remembered about Stephanie.  And I started going into this long science-y diatribe.  And she said, that's how you remember her?  And I thought, wow, that's weird.  But it makes sense.  When we think of our author friends who have died or artist friends, we think of their books and paintings.  And so when I think of Steph, I think of the replication of plasmid R6K in E. coli.  A plasmid is a ring of DNA.  In some ways, it's kind of a parasite inside a bacterial cell.  It's not required for the bacteria to live, but it consumes some of its resources to propagate itself in the bacterium.  The plasmid has components that ensures that, when a bacterial cell divides, both daughter cells get some copies of the plasmid.  (To be fair, though, to the plasmid, the plasmid can also give the bacteria some characteristics that help it, too, like resistance to antibiotics.)

We were studying how a specific plasmid, R6K, replicates inside a bacterial cell like E. coli.  DNA replication of the plasmid requires several different proteins.  One of the proteins is encoded by the plasmid itself and only functions for the plasmid - its only role is to turn on (and off) replication of the plasmid.  (You need to turn on replication so you have enough copies of the plasmid so that when the cell divides each daughter cell has one.  But you also have to turn off replication, or else all the cell will do is make plasmids until it's so full of plasmids it bursts and dies, and that doesn't help anyone.)  Plasmid replication also requires several host factors - which are proteins normally made by the cell as it lives.  But these proteins are co-opted by the plasmid.  Sort of like the way that a villain in a comic book will seize a toy factory and then convert it into a factory that makes awesome killer robots.  So in this metaphor, the plasmid is like a villain that captures a factory so it can make more... plasmids.  And in this analogy, the factory equipment is particular bacterial proteins, namely IHF and DnaA.  Steph studied IHF and I studied DnaA. 

IHF is this cool protein that binds and bends DNA.  You know how Superman can take a steel bar and bend it into a V-shape?  Well, IHF does the same sort of thing to a rod of DNA.  Which, it turns out, is very helpful in getting the DNA to replicate.

And, that, briefly, is what Steph dedicated five or six years of her life to studying.  I had to use to the word "studying" because that implies we were just reading something that someone else had found out.  No, no.  When I first joined Marcin's lab, he had invited members of my class of grad students to join him on "this great scientific journey".  Grad school really is about exploring, about discovering, about lifting up that rock that no one has ever lifted before, and finding the cool stuff underneath that no one has ever seen before.  In Steph's case it was figuring out exactly where in the DNA this protein, this IHF, bound.  And, of these various places it binds, which is most important.  (We do that by, one by one, mutating the so-called binding sites and seeing if the plasmid can still replicate. (You see that a protein recognizes a specific sequence in the DNA and when you change the sequence, the protein doesn't recognize it anymore and doesn't bind there.))

And that's what we did all day and all night every night for years.  When we weren't hanging out at her place, where she'd make me dinner and we'd read nerdy reports about DNA replication together and perfect the language of her newest scientific paper. 

But Steph and I did other stuff besides science.  She slow-danced with me when neither of us were dating anyone (which was most of grad school).  We went to see the Detroit Tigers play at the only Brewers game I ever went to.  We were together in the stands when the Wisconsin Badgers beat Michigan State - the last hard game before the Badgers went on to win the Rose Bowl that year (for the first time in decades).  Steph was torn, because Michigan State was her alma mater.  (These details may be wrong, but that's the way I remember it, so there.)  But one thing I will always appreciate her is comforting me and keeping me sane in the year after my mom died.  She was the first person I wrote to after my mom had passed away.  And one of our favorite songs of that time was "The River" by Bruce Springsteen, all about dashed hopes and broken dreams.  All those things that seemed so important, they vanished right into the air, Bruce sang.  And that's how I felt after my mom died, and Steph was my friend who helped me through that.  And, of course, grad school was hard (I compared it to marching through the desert eating sand all day, year after year).  And she helped me through that, too. 

I could ramble on about other things.  Like the They Might Be Giants concert we went to, together.  Or seeing Warren Zevon with Steph and shouting out "And his hair was perfect!" with thousands of other people.  Or the way she was really good at training and helping undergrads, while I wasn't.  Or that one time we wanted to hear "The Wreck of the Edmund Fitzgerald" (this was way before youtube or iTunes) so we called up the romantic late night radio show to request it and unsuccessfully tried to convince her to play it for us.  And I haven't even mentioned her guinea pig Spike.

But I'll leave it there.  Goodbye, Stephanie.  You were a good friend.  I will miss you.