Monday, April 22, 2013

Returning to Standard Life

My psyche may not be quite settled again, but it is now officially time to return to a more standard existence.  And by that, I mean the establishment of scientific and engineering standards.  I'm on my way, right now, out of the country over to the UK for the next SBOL standards development workshop.  SBOL expands to Synthetic Biology Open Language, and it's a community-driven effort to make it easier for practitioners of that science to exchange information about the systems they are building.  This applies to person-to-person communication, but also (perhaps more importantly) to communication from one computerized tool to another.  This latter is so important because building new organisms involves a lot of different types of information and processes, and it's hard for humans to track all of it correctly except for the very simplest of designs.  It also allows engineering services, like fabrication of new DNA, to be taken on by specialists who can take advantage of economies of scale to do them efficiently and cheaply.  The group at Newcastle is hosting this meeting, and we'll spend three days showing off our newest tools to each other and delving into such weighty topics as prioritization of working groups, standards body governance, interoperation with related standards, and extensions to handle additional types of knowledge.

Not long after I get back, I'll be hosting another standards discussion, the Workshop on Metrology for Mammalian Synthetic Biology that we're organizing in conjunction with the first Workshop on Mammalian Synthetic Biology.  At that one, we'll be asking a lot of really basic questions that don't yet have good answers, like "Who wants to know how a biological part behaves in a cell?", "What do we need to measure about its behavior?", and "How do we tell whether we got the measurement right?"  I expect the discussion will be much broader than just mammalian cells, but we needed to narrow the scope enough to have a productive discussion.  Mammalian cells also have some interesting properties that make them an attractive target: they're relatively big and tough, which seems to let them get less messed up by adding our new biological computing circuits into them, and there are also starting to be a lot of good mammalian biological computing components to choose from, which means we might soon be able to try to build much more complex systems.

In one sense, this type of work is boring.  After all, most of the process of getting things done is about having long dry arguments about tiny points of detail, and there's nothing inherently sexy about building better rulers or trying to agree on a data format that doesn't leave anybody too dissatisfied (consensus and satisfaction are necessarily opposed qualities).

That first impression is misleading, however.  Every scientific endeavor, no matter how sexy the topic may seem, has a lot of tedious work underlying it that is necessary to building a solid foundation.  Debugging code is never sexy.  Building makefiles and regression tests is never sexy.  Feeding mice or culturing cells or staring blankly at columns of data in Matlab is never sexy.  But you can't get where you need to go unless you do the hard work.  The alternative is to practice "slash and burn" science, where you go just far enough to get proof-of-concept results, then publish them with grandiose claims and move on to the next thing, leaving little for those who follow you to build on and yet making it difficult for them to do the work you ignored: "Didn't Smith and Jones already do that?"

When you get the unsexy parts right, you enable great things.  And standardization is a huge, huge, part of that.  Standards, and especially standards of measurement, are civilizational infrastructure.  Consider, for example, a 2x4 in your local hardware store: that humble piece of wood represents an absolute revolution in the construction and remodeling of houses.  Likewise, the next time that you chance to use a tape measure, think about how hard it is to make tape measures the same length.  How is it that you don't get different lengths of tape measures from different stores?  Why doesn't the length of tape measures drift over time as the machines used to make them slowly wear out? They do vary, of course, but a remarkably complex system of engineering mechanisms, professional associations, and government bureaucracy combine to ensure that you always have as many significant digits of length available as you need and are willing to pay for.

I didn't get into synthetic biology out of a desire to work on standards.  I got into synthetic biology to practice sexy cool mad science with living organisms.  Getting there from where we are today, however, will require that we build that depth of infrastructure that is so much needed and so often unappreciated.

Friday, April 19, 2013

I am proud of my city tonight

I am proud of my city tonight.

It has been a long and unusual day, locked down in our home while every law enforcement agent for a hundred miles was searching through Watertown for the second Marathon bomber.  Everything felt both nervous and detached at the same time: we weren't even technically in the lock-down zone, since we are just over the border away from Cambridge, but my office is in Cambridge, and it all just felt too close for comfort to go outside, and especially not with a baby.  Yet at the same time, I felt basically safe: one of the amazing things about our informational age is that I could be sitting here, in my apartment, and know the minute that something critical occurred, popping up in the feed on my computer or phone.  So I knew that nothing was likely to occur in our neighborhood.

Still, it's been with us all day.  It's why I quickly decided that today could not be a work day for me, not even from home.  There was simply too much on my mind, and I wanted to take my time here with my family and just be.  Last night, when the suspects killed Sean Collier, the MIT police officer who died, they did it right outside the building where I completed my Ph.D.  I know the spot well, having walked or biked across it many times.  The 7-11 they were reported to have robbed (though it seems to have turned out otherwise), it is right on the corner by the building where I meet my synthetic biology collaborators.  When they carjacked somebody over by Third Street, that is where I used to drive all the time, getting from my previous apartment to the lab and back.  The gas station where the carjacking victim escaped them is where I used to fuel up when I lived in Cambridgeport, right after undergrad.  The area the police were searching in Watertown is back behind where all the good Armenian bakeries are, and the place the suspect was finally caught is just a couple of blocks from where I bought my car.  The apartment where the brothers Tsarnaev lived?  Just 15 minutes walk from from us, on the other side of Inman Square.  So this whole drawn out incident feels very close to home, but at the same time almost surreal.  And I can still hear the helicopters overhead, as I have been able to since late morning.

So with all of this in the ambient, what is it that's making me proud of my city?  What makes me proud is the way that the city has responded.

I remember, after the attacks of September 11th, that my first thought was how scared I was of what our response would be as a nation.  What depths we might lower ourselves to, having been stung so badly by those attacks.  And I think that I was right to have feared that.

Here, from the moment when this attack occurred, there has been a sense of measured judgement and sympathy in the response of people.  Even while the first responders were delivering first aid, Bostonians came out of their homes to feed, warm, and house the stranded runners.  While CNN speculated wildly about Saudis, the local media has been rock solid, clearly distinguishing known and unknown, and getting us real information while never reporting rumor as news.  And then today...

Today, while a million citizens were shut up in their homes, the whole city seemed to me to feel like an embrace of "keep calm, carry on."  There's something scary and deadly going on out there, but we've put our trust in tax-funded professionals who are moving cautiously and deliberately.  People from within the search zone, sought out and interviewed by the media, really portrayed the best of Boston's tough but peaceful values.  And as the picture of the suspects continued to develop, I haven't yet heard anyone drop into xenophobic or Islamophobic rants.  Over and over, the direction goes more towards sorrow and sympathy, and a strength that has nothing to do with aggression or revenge.

That's something that I think we need to celebrate.  Our strength, as a free and liberal society, to find a place for the whole breadth of the world, in open celebrations of humanity like the Boston Marathon itself, and to hold and embrace that even in the face of what horrors the world can bring.  It takes a great moral courage and strength to do that, far more than it does to throw up walls to try to keep out the world and seek safety in isolation.  We have always been strong on the strength of our diversity, and even amidst tragedy and fear, I heard that strength in every word that came from Greater Boston today, all the way to the vast multi-ethnic crowd who lined the streets of Watertown after the suspect was arrested, and cheered every one of the officers who passed, thanking them for a safe resolution that even brought in the suspect still alive.

This city is old, by American standards.  It has deep roots and a proud history and attitude, and tonight I think it certainly has that right.

Monday, April 15, 2013

A Bad Day in Boston

Today has been a bad day in Boston.  I myself was nowhere near marathon, let alone near the finish line where the bombs went off.  Couldn't get through to my wife because the phones were down, and so even though I knew she wasn't planning to be anywhere near the marathon either, I still had all these pangs of fear and worry about her and Harriet until I actually made contact some hours after the bombs.  Poor Harriet was picking up on her parents stress, and having no idea what was going on, so we sat in the living room and one of us read aloud to distract and calm us adults while the other lay on the floor with Harriet, playing with her and making sure she didn't butt-hop her way into any hard table edges.

Something like this really rattles me, in a way that I find difficult to rationally explain.  It doesn't exactly scare me---an attack like today's bombing of the Boston Marathon is so random and so infrequent that I just can't figure out how one could be scared of it properly and yet still live one's life.  It would be like being scared of meteor strikes.  Not to say we can't do better at preventing such horrors, but I think we're likely dealing with the work of a deranged individual, not some organized cause, and in a modern technological society, there's only so much that can be done to limit the capability of individuals to do harm.  The only way to make society overall safer from this sort of attacker is to make sure that less people slip through the cracks of isolation, alienation, and mental illness---a long, hard, and complex process, sure to be opposed by those who think that all somebody needs to do is "pull themselves up by their bootstraps" or to "act like an adult."  There's a lot of emotionally wounded adults out there, and today there are many more.  No good, and nothing much that we can do but carry on, live our lives as constructively and humanely as we can, and grieve when we need to grieve.

Stay safe, everybody, and live well both today and for all your hopeful tomorrows.

Tuesday, April 09, 2013

What Sort of Careers Do Tiggers Like?

Yesterday was a day at DARPA (of which I shan't speak further, since it was all about possible future projects).   On the way back, though, I had a conversation that made me really happy.  Sitting next to me on the plane was a young man, part of a high school trip that had come down to see the capital as part of their AP Government class.  As we started talking (his classmates congratulating him on starting conversations with strangers), I also learned that he was a senior, wanting to become an engineer, and thinking about UMass Amherst (a worthy school indeed), though a little boggled by all the possibilities of departure from home into the wild world of undergrad. So I shared a bit more about myself and my life as a scientist, and we had a pleasant though somewhat lopsided conversation.

What I really want to share with you, though, dear readers, is one thing that came up as we talked, a metaphor that have I found extremely helpful in those times when I am figuring out what I want to do with my life, professionally or otherwise: what do Tiggers like?

This comes from an old Winnie-the-Pooh story (by which I mean A.A. Milne, as I do not accept the validity of the Disney interpretations in my personal canon).  In the story, the newly arrived Tigger is hungry, and the other animals offer to get him food.  Only problem is, Tigger isn't sure what it is that he likes to eat!  The generous Pooh allows that he might share some of his honey, and Tigger immediately responds that "Of course, of course!  Tiggers just love to eat honey!"  But the honey is too sweet, so Eeyore offers his own favorite dish of thistles.  "Of course, of course!  Tiggers just love to eat thistles!" And thistles, of course, are too spiky.  So it goes, throughout all the animals, until finally Kanga offers Roo's nasty medicine, which proves exactly to Tigger's taste.

I find this quite instructive as a life lesson.

The moral, as I see it: when you have lots of plausible options, don't be paralyzed trying to figure out which is the best to do.  Just do things.  Do worthy things, that you do with passion and persistence.  You can always change course later if you have to, and having given it your best in the mean time, you will not suffer badly for it.

Tuesday, April 02, 2013

An Evening Celebrating Science

Last week was the annual Science Development Program Dinner at BBN.  The SDP is a complex and unusual institution at the company, one of the things that I think makes it pretty unique.  Generally speaking, it's an umbrella promoting all of the more academic-style aspects of the company, like journal publication, hosting visiting scientists, running seminar series, teaching university courses and supervising students, professional service on committees and editorial boards.  It also runs the pseudo-tenure process for promotion on our scientific career track, a set of senior ranks parallel to the management track.

I think the SDP is a very important thing for keeping the culture of BBN, riding on the edge it does between academia and more traditional industry.  And once a year, the company throws a party to celebrate its scientific side, and to reflect on where we have been and where we are going, scientifically.  Everybody who has done significant SDP activity in the past year is invited, and over the course of the program we hear about it all.

This year, we also remembered Wally Feurzeig, who just passed away after 50 years of AI research at BBN.  He was somebody who touched my life decades before I even knew his name, as one of the inventors of the LOGO programming language, which I spent many happy hours making pictures with in elementary school, without even realizing the ways it was teaching me about algorithms.  I also heard a story about one of our founders, Leo Beranek, long ago "retired" but still working on his own as a scientist at age 98: he will apparently be presenting a couple of papers at the same Acoustical Society conference as my wife in a couple of months, not as some sort of "aged and distinguished speaker" talk, but as ordinary peer-reviewed scientific papers.

I find these things inspiring.  I find the whole event inspiring, in the way that it invites me to step back from the hustle and bustle of daily deadlines and the money chase, and to renew myself at the well of scientific thought and the importance of inquiry for lasting impact and also for its own sake.  It's an important part of why I am working where I am, and what brings other people I want to work with there as well.