Author: martha

Tuesday was my first WUS back in a long time — being injured is so isolating and lonely — and after my recent work travails a good dose of WUS was exactly what the doctor ordered.

WUSsies were popping up like daisies after a spring rain: we had Justine post-baby, and Ryon post-concussion and face-splitting (25 stitches, was it?), and Vishal post-shoulder dislocating Glover Park steps tumble; we had Sophie from Charlottesville and a new guy from Colorado — we nearly expected Amy to swoop in from Portland;  Sabrina is back for a couple summer months; Tracy made a rare appearance with Keith; and I don’t even have space to list the whole boatload of WUS regulars that showed.  Good luck to the other CPBGers trying to catch the NBA finals on the television — the roof deck was ours.

So good to catch up on all the crazy WUSsie news.  We got weddings galore and babies born and getting ready for their world debut (Neal & Gaby’s boy is gunning for October).  And what’s this with BOBBY GILL getting hitched?  Wasn’t it was just a year ago he was drooling over my Italianos?  Maybe we’ll have to have a Beer Mile just to lure him out to confirm the rumors.

WUSsies been tearing it up.  This is the best picture I’ve seen in a while.  You just gotta love Joe Clapper.

On this blog I’ve made numerous indirect references to my job (e.g., postings my work trips to China, Istanbul, and Kathmandu; NIH 5k runs; and of course the famous colleagues from Italy, Alice & Isabella).  But I haven’t written much about what I actually do for my job, mainly because it never related much to running except for taking me to cool new places to run.  But this this weekend was different, on Saturday my work and running worlds fully collided.  I was entirely planning to run a 4-mile PR Twilight Race in Ashburn at 7:30pm on Saturday night.  But work was making me, as my Jewish mom would say, meshugana (meshugana is yiddish for crazy person; my mom tends to use it more to mean a temporary crazy spell).  And to explain why I’d gone meshugana I have to relate a little about what I actually do for a living besides constantly travel to exotic countries.

Most people know that I’m a biologist who studies viruses at the NIH.  Some can elaborate that I don’t do ‘wet lab’ (ie anything that involves a pipet or rubber gloves) but do computer analysis of the genetic sequences of rapidly evolving RNA viruses like influenza.  Those who get extra big cookies can say that studying the evolution of influenza viruses is important for several reasons: (a) the virus evolves so quickly that the influenza vaccine must be updated annually with new strains, and predicting new strains remains a major public health challenge, and (b) there is a lot about the seasonality and spatial spread of influenza that we still don’t understand, and you can use genetic data to study spatial and epidemiological patterns in very fine detail.  Since the 2009 swine-origin influenza pandemic, I’ve been studying influenza increasingly in pigs.

I love so many aspects of my job — I have a lot of freedom to follow my curiosity and pick my own projects, and to work in various locations — home, West Virginia, with my PhD adviser at Penn State, or in my lovely little office in an old mansion on the NIH campus, I have really wonderful colleagues (Alice and Isabella as cases in point), and I get to travel to very cool places to collaborate on work projects.  But there is one part of my job that drives me nutty, hair-pulling nutty, and that is Bayesian analysis.

The crux of my work involving inferring phylogenetic trees from hundreds of viral sequences to visualize the evolutionary history of the viruses and how viruses collected at different times and in difference geographical places are related. [For the very, very few of you interested in more detail, a nice review of the applications of evolutionary analysis of influenza to uncover basic viral characteristics like seasonality, spatial spread, and drug resistance is available: nelson-holmes-evolution-epidemic-influenza-NRG-07].  Phylogenetic trees (such as the classic one showing the genetic relatedness of humans, chimps, gorillas, and other apes) are central to the concept of evolution and even Darwin sketched a loose vision of a phylogenetic tree in his notebooks to explain the notion of common ancestry among organisms.

There are many different computational methods for inferring a phylogenetic tree, with the general trade-off being that slower, more computationally intensive methods generally more accurate trees, while quick-and-dirty methods are faster but make more assumptions.  Currently in vogue are Bayesian trees that incorporate prior assumptions (based on empirical evidence) and that produce not a single tree but an entire distribution of trees (generally 10,000 or so) with different probabilities of being the ‘real’ tree.  The Markov chain Monte Carlo (MCMC) algorithm is a nifty, commonly used algorithm that searches through ‘tree space’ to assess the probability of different trees.  There are various convergence statistics that determine whether the chain has been run long enough (anywhere from 5 million – 100 million or more iterations) to reach convergence.  You can endlessly fiddle with various parameters of your model to try to improve the rate of convergence, you can use different sized data sets, you can practice all kinds of black wizardry, or you can act like a toddler and mope, cry, tantrum, despair, and refuse to run 4-mile races.  I generally opt for the latter.

I am not a technically savvy person.  If Aaron adjusts all the settings on the camera, I’ll point and click it.  I never even bought a home printer because I was convinced I would never get it to work.  You all know I don’t use GPS or heart monitors or even watches.  I’m a shameless luddite.  So how did someone as technically Stone Age as I end up in a job that primarily involves extremely complicated computational analysis?  I ask myself that on a regular basis.  What was I thinking??  Why didn’t I choose something I was marginally competent at for a career?   The problem is that I’m obsessed with the fascinating underlying scientific questions.  Viral evolution is remarkable — the different strategies viruses have for successfully transmitting, infecting, and replicating in various different species of host.  The speed at which viruses adapt to different selective pressures, and the constraints on evolution and trade-offs.  These miniscule packets of genetic information (influenza virus has a ~12kbp genome encoding for 11 genes, while the average genome of tiny bacteria is ~5,000 Kbp) that are able to thrive in so many species.  Rabies is the most amazing — the way the virus actually induces dramatic neurological changes in the host (rampages of biting) to perpetuate the virus’s own transmission.  And now modern sequencing technology continues to advance each year allows for unprecedented study of how these tiny genomes evolve, and how the evolution is being driven by changes in ecology, agricultural practices, and human demography and behavior.  And not only does understanding the evolutionary dynamics of viruses have major implications for human health, but also reveals basic evolutionary processes of natural selection and random genetic drift that are far easier to study at these restricted scales than in humans or even bacteria and is our best weapon against the anti-evolution radical Christian factions.

I think I would be able to tolerate being bad at a job that I love conceptually while being technically incompetent (or sub-par, whatever) if I weren’t….well, me.  I’ve always had a hard time swallowing the feeling of disappointing others — something I thought I would shed over time, like one of those teenage pimples you thought you were done with at 16 but that still erupts at 30.  It manifests in running, too.  I’m still stupidly sensitive to the sinking feeling of being a disappointment.  I don’t understand how I can still feel the same way I did at age 30 as I did as a child, hanging my head after a soccer game lost.  When do we get over these things?  And when do we stop going for our own jugulars at the slightest whiff of failure?  It’s funny, when I race my little silent self pep talk is one simple request to my head to just please stay out of the way, to just be quiet, to not fire its fusillade of negative thoughts that I’ll have to spend a good part of the race just trying to stamp out.  Well, we’ll save a detailed discussion of what my brain tries to do to me while racing for another day — there’s a lot of backstory there.  Heck, I think Brian Greeley could fill a neuroscience thesis on the places my head goes when the gun goes off.

 

 

 

 

 

 

Run for the Birds

1-mile, 2-mile, 5-mile, and 7-mile options

Shepherdstown, WV

 

 

‘Sean, you’re running this?’  The incredulous volunteer apparently did not consider the 11th annual Shepherdstown Run for the Birds to be a race befitting the likes of the Great Sean Andrish.

I retorted that the Run for the Birds was the premier event of the spring, a claim that Aaron and Sean understood by the end of the day to not be the least hyperbolic.  RFB is a little gem of a race, with 5- and 8-mile trail race options that wind along the roads, fields, and woodlands of the US Fish & Wildlife Service conservation training grounds in Shepherdstown, WV.  It’s a low-key family friendly affair, with a 2-mile fun run that my dad did, as well as a 1-mile kiddie run that Selena’s three boys ran, following a lengthy warmup of calisthenics (see little Emmett demoing his killer yoga moves).

I was originally signed up for the 8-mile trail race, but I had been limping all week since the Boston Marathon, with a lot of pain in my IT band and the outside of my left knee.  I had found that skipping and cantering did not cause it pain, so I changed to the 5-mile race and was prepared to skip my way through the five miles if I had to.  Sean signed up for the 8-mile; the last time he could recall doing a short-distance race was 2005.  And Aaron was psyched to skip and prance the 5-mile version with me.

 

But I have curious legs.  They griped at the beginning of the race while I was running cautiously, but they got much happier as the pace picked up and by the last mile I my knee was pretty much pain-free.  Although poor Aaron was robbed of what was supposed to be an easy frolic through the fields and instead had to sprint through the woods with me.  I didn’t want to run fast, but my knee demanded pace, so I complied.

The course is a series of different loops of small rolling hills along a road, then through fields that feel a lot like a XC course, and then along a wide dirt path that twists through the woods.  There is one big hill, that ends with unnecessary cruelty through some tall grass.  We always have an internal competition to see who can spot the most birds along the course.  No one else was looking so I won that.  I also won the 5-mile race, as did Aaron (we finished together 1-2), and Sean won the 8-mile handily, leading start to finish.  WUSsie domination.

 

While I love a lot of things about the RFB — the fun course, the low-key atmosphere, the good cause (Potomac Audubon Society), the 4 difference races to accommodate all ages and kinds of runners, the plethora of friendly volunteers — the perennial weakness of the race is the awards ceremony.  It takes them hours to compile the results — the race started and 9am and we didn’t get out of there until noon, and awards were still being handed out when we left.  I guess it’s part of the charm of the race.  The prizes are also pretty ghetto: a slip of paper for free entry to next year’s RFB.  (Although I guess that’s better than the Fire on the Mountain prize — Aaron and I actually ran into the FOTM RD at race registration, and he sheepishly admitted to still being ‘backlogged’.  It’s been 6 months, buddy.)  But I had 16 guests arriving at 1pm for a post-race birthday lobster party that I had done zero preparation for……

 

Except fortunately we had gone to Wegmans the night before (there is a Wegmans in Frederick, MD), and Wegmans has everything a girl could possibly want for a birthday party, including a frog piñata.  When my friends arrived I was still madly cooking and still in my sweating running clothes, but there wasn’t much point showering when the day would be spent playing tennis, romping in the woods (we had to have the traditional Birthday Bug hunt — yes, that is exactly what it sounds like: here’s your jar, go get your bugs!! — Leo won this year with a pretty awesome grasshopper), smacking the piñata, and cracking open and eating lobsters — which, at least the way I do it, is a pretty messy affair.

The weather held for us to enjoy our lobsters in the sun.  It was a rollicking good birthday.  Sean and Cori even cracked their own lobsters this year.  The kiddies were all good sports: Lily and Aidan even helped Sean pick out all the rubber bands out of the pounds of lobster shells so we could throw them in the compost out back.  In addition to what have become the lobster party regulars — Cecile, Bernard, Cori, Jess, Josh, Tany, Bing, and Sean — we had Selena and her family, Wladimir and Cynthia from Brazil, Cori’s niece and nephew, my uncle Jon, and my boss Mark, who actually owns a property in Shepherdstown that with all his jetsetting he hasn’t had a chance to visit yet.  But maybe after seeing the charms of this quiet riverside West Virginia countryside he’ll go check it out some day.

 

Bull Run Run

April 14, 2012

 

Normally Aaron is photographer extraordinaire.  But this year he was going into Boston untrained on account of his Achilles and didn’t want to stand around all day.  And he had a whiny girlfriend who moans about rising before 6.  Plus, this year we had Bobby ‘So you got a new dog?’ Gill to fill in.  (Yes, that was my not-so-subtle way of inquiring who his new lady friend holding the leash at his side was, as Bobby had allowed 30 minutes to lapse without any sign of an introduction.)  Aaron and I were happy to simply be photo back-up, sleeping in til good ole 6:30am and just camping out the whole day at the Marina.  Compared to working the whole night at Visitors Center at MMT (my only other volunteering experience), shooting pics at BRR was easy peasy.  And fun.  By mile 77 at MMT I see a WUSsie come through every couple hours.  At Bull Run it was rapid fire — Neal, JLD, Sean, Keith, Mario, New Guy Mike, Michele, Doug, Kerry, Joe, Boots, Kirstin, in something like that order.  And unlike MMT, these runners looked HAPPY.  And it was SUNNY.  Ooh, I think I found my new volunteer calling.  I actually won’t be able to volunteer at MMT this year because I’ll be flying to London for work.  I will miss it — that is certainly a unique experience up there, the closest you get to feeling like a nurse on the Civil War battlefield.  But not only do I like sitting all day in the sun (I found a perfect log to plop on), it turns out that I really like to take pictures.  (The rest of our pictures are here).