Sunday, December 14, 2014

Discovering Luxembourg

I think that I am falling in love with the architecture of Luxembourg.  This morning I have spent mostly walking around the streets of the city, with its curious mixture of old and new, and I am being continually taken in by the drama and beauty of the place.  My hotel was right in the center of the city, and the city itself is quite compact: a hill surrounded by deep and defensible valleys, now bridged with great stone and concrete viaducts that carry highways and rail lines.

The streets in many places are nearly as narrow as Venice, but with high 18th century-style buildings more reminiscent of Paris.  Even the newer construction often seems to have chosen either to fit in or to coherently and deliberately depart (and there is quite a bit of new architecture, Luxembourg having apparently been rather damaged in the tail end of World War II).  Moreover, since the center is much more compact than either Paris or Venice, all these things combine to create a city where even a short walk turns around many corners of surprises, dramatic angles formed of the corners and confluences of little wriggling streets.  At the edge of the hill, the city drops off sharply, with steep stairs and roads plunging down into the parkland of the river valley.  Along the side of the valley are old castles, pastel-colored stone houses marching down the side of the slope, and even homes driven into the rock itself.  On the far side rise cranes and the glass towers of the country's industry, though I'm not sure whether those particular towers hold banking or software or European government.

It is a rather international city as well, as befits a small country that attempted neutrality for a long time, then after its experience in World War II turned about and fiercely embraced the new order that it helped to create, as one of the founders and agitators for both the European Union and NATO.  I walked along a major road named Franklin D. Roosevelt Boulevard, and not far away is another street named for John F Kennedy. I hear many languages in the streets, and see at least at least a smattering of cross-cultural couples.  Nearly every advertisement that I have seen has something to do with the way the country sees itself as a crossroads, a place not on its own, but defined through its connections with the rest of the world.  Luxembourg intrigues me, and I need to come here again with more time to spend.

Now, I am sitting on the steps of a public building on the edge of one of the city squares, listening to blacksmiths pounding out ornaments in the bustling Christmas market in front of me, and amazed to find myself automatically online (perhaps it is the university) so I can even upload this post while it is fresh on my mind.  Good job, Luxembourg: yet another way I like you.

Saturday, December 13, 2014

International Showers

Somewhere, inside pretty much every international airport, there is a place where you can get a shower.  Sometimes they are public and anybody can get at them; other times you have to get access to one of the airline lounges, either by being a frequent flyer or paying for a day pass.  If you can get at that shower, though, it can make a world of difference.  Last night, before getting on my overnight flight from Miami to London, I got a shower in the American Airlines lounge, making up for not really being able to clean my hair properly for the last week.  Then, while waiting to connect in Heathrow, I got another shower in the British Airways lounge, and washed away all of that red-eye flight nastiness that builds up when you've spent a night neither really sleeping nor not sleeping.  In both showers, the water temperature was kind of unstable (each in its own special way), but who cares: it was a few minutes of perfect quiet solitude and self-care, and by the time I stepped out, I was clean from my toes to my teeth and with a much more settled and stable mind, ready to face the next step of my voyage.

Thursday, November 20, 2014

Hati goes on a trip

I just had a (very) quick trip to Boston.  Harriet was disappointed that she couldn't go with me, so she sent a representative...

Hati was very excited to get on the airplane with daddy to go to Boston.  What would they find?

In Boston, Hati and daddy went to stay with friends in a nice house. Hati had hummus and ruti and ate angur.

Hati also found good books to read.

When daddy called home to Harriet, Hati sat on Daddy's shoulder to listen to the conversation.

Later, Hati got to ride on the subway with Daddy.

They met some of daddy's friends and ate chocolate and berries to celebrate a paper they had published. Hati got to eat some too.

Then it was time to go back to their room and go to bed.

The next day, Hati went with Daddy to his office. Daddy had a very big computer.

He spent the whole morning talking to people. Sometimes it was interesting and other times Hati was very bored.

At lunch time, they went in a car to another office, where Daddy told people about his project, and Hati got to eat a cookie.

After that, it was time to go to the airport and go back to Iowa.

Finally, Hati and Daddy got back to Iowa. It was very late, and Hati fell asleep in the carseat, happy to be almost home.

Tuesday, November 04, 2014

Heart is the best power

Yesterday at the iGEM awards, I had another massive experience that took me completely by surprise.  This year, they introduced a new award, The Chairman's Award, which is picked by Randy Rettberg (the chair) as the team who best represents the spirit of the iGEM event: curiosity, hard work, intellectual honesty, etc.  When he headed up to give it, as the penultimate award before the top prizes, he told me: "Why don't you come up too... you know the team."

And so it was that I came to be onstage again, once again in front of that massive audience of 2500 genetic engineers from around the world, to shake hands with our wonderful scrappy underdog team from Sumbawa, Indonesia, and give a totally unprepared and off the cuff speech in praise of their outstanding efforts.

I talked about how I was proud and humbled by having them in our new measurement track.
I talked about how, when I spent time talking with them at their poster, they told me "We are new, but we have confidence because have great heart."
I talked about how they were doing real genetic engineering addressing real problems in their local community, at a university that was only one year old.
I talked about how they were worried they could not be a measurement team, because their cell phone cameras could not measure green fluorescence.  We told them a negative result was still a useful result, and they sent us beautiful documentation of the fact that their cell phone cameras measured all the samples the same.
I talked about how they had engaged the local community, teaching honey farmers to pipette and helping them understand synthetic biology and its potential value in their lives.
I talked about how they had gotten religious support for their genetic engineering from the local imam and the local priest.
I'm crying again just writing about it.

I hope that somebody was taking a video, because I'd like to share it with you.  More importantly, however, I want to stop talking, and let you see them explain their project in their own words:

Monday, November 03, 2014

To all my peeps at iGEM

I just gave a scientific talk before the largest audience that I have ever in my life addressed: 2500 synthetic biologists at the iGEM jamboree. In a five minute talk, I told everybody about the gigantic interlaboratory study that we ran this year, including a special shout-out to the team from Sumbawa, Indonesia, who did their measurements using cell-phone cameras because the nearest fluorescence-measurement equipment was 1000 km away.

And what did we get?  From 45 teams in 18 different countries, we got a worldwide baseline and some remarkably good consistency in measurement values:

Next step: write it up and plan for next year's study...

Tuesday, October 07, 2014

Wednesday, October 01, 2014

A triumph of citizen science at iGEM

I recently had one of those rare moments of true elation, a scientific triumph that actually brought tears to my eyes. It's my triumph, but it also belongs to so many more people than just myself, the biggest experiment that I have ever run in my entire life.

Let me back up a bit and explain.  Every year for the past 10 years, there has been a big event called iGEM - a genetic engineering "jamboree" in which undergraduates spend the summer doing synthetic biology projects, then get together in the fall to show each other what they've done, compare results, and compete for who has done the most awesome project and presentation.  It started small, but grew quite quickly, and this year there are on the order of 250 teams participating from all around the world.

Last year, I started talking with the iGEM organizers about the possibility of starting up a new track in the competition, focused on the problems of measurement.  I've never really been interested in measurement as a subject, myself, but I've found that I am getting more and more invested simply from a need to have good data in order to accomplish the things I want to do scientifically.  Putting together a measurement track at iGEM sounded like an interesting idea, and one of the things that made me more interested was the idea that we might ask the teams in the measurement track to participate in an interlab study.  In other words, have a bunch of different labs do the same experiment, so that we could compare data and see how reliable the numbers actually are.  So I put together a nice diverse team of colleagues interested in the idea: Traci Haddock (Boston University) is a close collaborator on precision characterization and genetic engineering, Jim Hollenhorst (Agilent) is a long-time veteran of instrument development, and Marc Salit and Sarah Munro (NIST) are specialists in measurements and standards.  Together we worked with the folks at iGEM HQ, especially Kim de Mora and Meagan Lizarazo, to put a track together.  And then we sat and hoped that people would register.

I was worried we'd have only a couple of teams sign up, and that we'd end in an embarrassing fizzle, but Kim and Meagan kept telling me not to underestimate the iGEM students, and so I kept my fingers crossed.  Almost nobody registered and almost nobody registered... and then the deadline for teams to pick tracks came and suddenly we had 11 teams dedicating their summers to the study and improvement of the science and engineering of measurement.  And the interlab study... well, the best way to show who signed up is to show the map I put together:
Teams participating in the iGEM 2014 Interlab Study
(interactive online version) 
That's 45 teams who signed up, just because they believed that it was important to understand how well we can compare our measurements.  Teams not just from America and Europe, but from all over the world: from Mexico and Colombia and Brazil and Turkey and Kazakhstan and China and Indonesia and on and on. Students who decided to take time away from their main projects, because they thought that this would be fun and important.  Who listened to us and understood, when we explained about the value of repeatability in science, and the importance of building our knowledge on a solid foundation.

So that was the first time that I was blown away.  But we didn't know what would happen when we got the data.  As this was the first year that we did any sort of interlab study, we didn't know what teams would be capable of, what equipment they would have, what cells they would be working with, what knowledge and guidance their supervisors would be able to produce.  So we asked for just a simple thing, to measure three genetic constructs in simple, standard conditions.  We hoped that some teams would be able to do some of the more sophisticated techniques that I have been applying, but knew that they might not be able to.  But we had no idea what quality of data we might actually get.  iGEM is somewhat polarizing in the world of synthetic biology: there are a lot of professors who think that it is wonderful, and who build research programs that are intimately tied with things their students do in iGEM.  Others, including some very high profile researchers, think it's a waste of time and that they can't trust data produced by undergraduates, and won't have anything to do with it.  Me?  I hadn't committed to a position yet: iGEM certainly looked really neat, and I thought the participating students all get an excellent educational experience (which is enough to recommend it right there!), but I'd never been engaged deeply enough to know how sound the science that came out of it was.  Here, as the data came in, I might finally begin to learn.

Saturday afternoon, with data from 2/3 of the teams in hand, Traci and I sat down in a corner of the meeting we were at to find out what we had wrought.  I opened up an Excel spreadsheet and she parsed through the worksheets the teams had sent in to read me out their vital numbers.  The columns filled, and it was clear that some of the teams had gotten reasonable data while others had run into problems---failed cloning or contamination or instrument problems or who knows what.  No surprises there---it would have been surprising if nobody had had trouble. And when we had enough entries in the table, I selected a couple of columns and told Excel to make a plot.

Disappointment scattered itself all over the graph.  Where we would hope to see a nice straight line of points, there was a virtual cloud of incoherence.  Every single graph we tried looked like that: a massive mess of scattered hash.  Looking into the methods sections of the teams' reports, we could see a number of differences, both large and small, and so contented ourselves with the idea that we'd been able to actually quantify just how bad is the effect of lab-to-lab differences in the way that people work with cells and instruments.  Not a bad result, especially for an experiment whose basic aim was to establish a baseline from which to work.

But then... then on the plane back from Boston, I moved the data from Excel to Matlab, where I could really analyze the numbers, and I plotted them again.  And it all lined up.  I had selected the data points to use by a simple rubric for likely validity of the data: are the "high", "medium", and "low" expression promoters in the right order and showing at least some significant difference?  That helped a lot, but even when I included everything, it was nothing like the mess we'd seen before.  I looked again, and discovered that nobody on Earth should ever use Excel to analyze any sort of data.  Those plots that looked so horrible?  That's was because Excel was experiencing an odd bug that caused it to use row numbers for the X axis on the graph rather than the actual values it claimed to be plotting there.  If you replace one of your two variables with arbitrary junk, well of course it's going to be a mess.  But the real data... the real data was so nice.

And that's the thing about science, really, that's sometimes so hard to wrap my head around.  It works.  The universe really does run on rules, and no matter how strange or complicated or hard to understand a thing may be, the substance of reality has no mystical component.  If you can just find the right lever and the right place to stand, everything makes sense, and this fact is indicated by the fact that these points of data make a beautiful line.  It doesn't matter whether we want the result we get or not, and there is no moral implication in the knowledge: what we do about the universe once we understand it is where our humanity comes in.  But even life itself has rules, that we can understand and work with, and this experiment---so simple, yet at the same time so large and complicated---is another step towards doing that.  

What exactly were those results, you ask? Well, I'm sorry, but you're going to have to wait.  We've promised all the teams that we're going to announce the results of the study at the iGEM jamboree at beginning of November, and nobody gets a peek before then.  All I can say for now is: it was worth it, and I am humbled by the remarkable enthusiasm and dedication of young men and women from all around the world who made it possible.

Saturday, September 06, 2014

Creative versus Scientific Writing

I listen regularly to a podcast called "Writing Excuses," about all sorts of aspects of being a professional author of fiction. It has the wonderful tagline, "15 minutes long, because you're in a hurry and we're not that smart."  Of course, the folks on it are pretty smart, but the 15 minute format does well for them I think, because it forces them to focus tightly on the key ideas that they want to communicate and think about, rather than allowing the meandering self-indulgence that I have encountered on many a longer podcast. I listen because one of my favorite authors is one of the podcasters, because I enjoy listening to the banter and their description of an alternate world they live in right beside my own, because it's precisely the length of one bicycle ride to work, and because I find it to be surprisingly relevant to my own professional life and identity.

As a scientist, one of the things I do is that I need to be constantly able to write.  Last year, for example, Google Scholar says that I generated 19 scientific publications, by its somewhat loose standards.  Besides these, of course, there's a number of white papers and proposals and reports and talks and all the rest of the miscellany that comes as part of professional communication.  Those documents span a surprising number of years as well, with the oldest amongst them having been drafted in 2008 and the youngest only a few weeks before its publication.

Together, those 19 publications comprise a total of 214 pages, of which 102 pages and 14 publications are ordinary scientific papers. The remaining five are standards documents or patents, which get rather inflated because they play by entirely different rules of what counts as a good document: a scientific publication must communicate, while a standards document is intended to constrain the bounds of a complex technical activity and a patent aims to noisomely mark the largest possible territory with legal spoor.  Estimating based on the typical density of 500-900 words per page in scientific papers, that's around 66,000 words of ordinary scientific papers (not standards or patents).  The papers average 3.6 authors each, or 3.1 if I exclude those authors who did no writing.  Interestingly, many of the higher-author papers are also shorter, so if I allocate pages by authors on a per-paper basis, I find that about 29,000 words of scientific publication are attributable to me in 2013.

Interestingly, that's actually much smaller than I would have thought, about 1/3 of a typical paperback novel.  When I compare it with writing that I've done in non-scientific contexts, it is actually surprisingly similar.  For example, the last major live-action roleplaying game that I ran---a 10 day long affair called "Harry Potter Year 7: Hogwarts Under Siege"---was about 490,000 words, according to a quick check of the LaTeX source in its repository.  That was written by six authors over the course of two years, meaning about 41,000 words per year are attributable to me.

Apparently, if I were a novelist, I would produce about one paperback every two years.  But I wonder if that's really a fair comparison or not.  It's tempting to say "No, because science..." but then I look at the roleplaying game number, which I had honestly thought would be much higher.  Even that roleplaying game is very dense with research and cross-links, but then, so are many novels.  I think about the authors on that podcast, who also do a lot of careful background research---one is known for his intricate magic systems, another writes fantastically precise period pieces, another does a lot of math in the course of producing good, consistent hard SF.

So honestly, I think that I should view myself as simply a rather pokey writer, by professional writer standards.  My favorite authors are probably all writing about four times as fast as me, if that comparison is something that is actually meaningful.

The real question is: should I care about it?  I'm not sure.  I do think that my writing is less efficient that I would like it to be, and looking at the numbers, I think that there is reason to expect that I should actually care to improve it, if only so that I can spend less time in my "frustrated" stages of writing.  In that sense, I spend a lot of time on certain sentences in a document, while other whole sections go much faster, and much of that time is spent in a certain type of paralysis, going back and forth between two or three ways of presenting the same idea, writing and erasing and rewriting and chopping it up and back and forth and so on.  I'm sure that there are cases where that level of precision can actually matter, but certainly not at the first draft stage.

The writers on the podcast that I listen to will often say, "Writing is what defines a writer. If you write, then you are a writer."  Just write.  Put it down, correct it later.  Some exercises for myself, I think... dear readers, I will let you know how it goes.

And, hmm. This was not the direction that I expected to go when I had started to write this morning.  I suppose that this is one of the charms of scientific writing, even in a casual and informal venue such as this.  No pre-publication peer review to put out these ~900 words, however, just the post-publication review of comments and who out there finds it actually interesting enough to spend their precious time to read.  And now, in honor of my drifting topics:
Harriet, already prepared for receiving scientific reviews.

Tuesday, September 02, 2014

The Engineers' Song (clean version)

As I wrote in my last post, I found it quite unexpectedly distressing that I couldn't teach the Engineer's Drinking Song to my two-year-old without feeling rather much uncomfortable.  Now, maybe this shouldn't have surprised me at all, I mean, it is a drinking song and says so right there upon the title. But what I really like about it is the catchy tune and upbeat rhythm, which contrast quite strongly with the misogynistic and self-hating nature of the lyrics.  Have a listen and see: this video is about as clean as it gets, being performed for prospective students and all.  And I suppose that this is all to be expected from a drinking song originally from the military and then adopted by stressed out undergraduates, both of which are groups highly invested in being crass for different reasons.  I can appreciate a good bit of crassness myself, but it has its places and times, and singing to toddlers is not one of them.

But I'm really proud to be an engineer, and I think that it would be nice to have a version of that catchy tune that's positive and celebrates the things I value about my life as an engineer, and that I'd like to pass on for another generation. And so, dear readers, in the spirit of Broader Impacts and promotion of STEM field education, I present the following revised collection of lyrics, and in the spirit of our tinkering lives, I invite you all to suggest lyrical improvements, additional verses, and to spread it to the winds:

The Engineers' Song (clean)

We are, we are, we are, we are, we are the Engineers 
We can, we can, we can, we can, make anything with gears
Computers, lasers, DNA, just come along with us,
'Cause anything that we can dream, we'll build without a fuss

An engineer's an engineer from when she first can talk,
While other kids look on with awe, she's stacking up the blocks
The simple phrase "How does it work?" sets fear in parents' hearts
"Go hide the drills and screwdrivers, she'll take it all apart!"

Grace Hopper was the first to tame computers to our will
By making up compilers that let any Jack or Jill
Build network applications at a wild frenetic pace
So any time you use your phone you'd best remember Grace

When someone hires an engineer they know what they will get
A bunch of smarts and knowledge and a willingness to bet
But supervise them carefully and check what they have done,
'Cause otherwise the engineer will just build something fun

Oh, Tesla was an engineer of electricity
with coils and sparks and deathray plans as far as you could see
And when his rival Edison had lost the current war,
Well, Telsa just went to back to work on radio and more

A barbeque was going fine 'til someone dropped a match,
And set off an explosion from where lighter fluid splashed
While everybody else had panic running through their brain
The engineer said "Get some more and let's try that again!"

In great New York the Brooklyn bridge was rising every day,
The old man who'd designed it had just died and passed away
So Emily Roebling stood up and she said, "It's not so hard,"
"I've an engineering spirit, never mind what's on my card."

An engineer and sales rep were a-walking in the park,
The sales rep pitched a product that he thought would be a lark
The engineer was skeptical until he set her right,
And told her that the product would have lots of blinking lights

An engineer retired after a long and full career
Her husband asked her afterward "What will you do now dear?"
She turned back to her husband with a smile lit like the sun
"My love you know, now I'll have time to get some real work done."

Saturday, August 30, 2014

Challenges in the Raising of Engineers

My morning, today, started in an unusual and rather unexpected way.  Slowly waking on a lazy Saturday morning, I could tell that Harriet was already up because she was banging on her door, trying to figure out the child-safe sleeve around the handle that we use to keep her in her room while she's still too young to be trusted around the stairs alone.  Little did I know that it could go the other way as well. When I arrived to open my two-year old daughters' door, I found it solidly locked against me, and Harriet giggling at my inability to open it.

Now this, of course, should not pose a problem at all.  Every standard internal door with the little push-button locks has a hole on the other side where you can push a pin or screwdriver in and pop them open.  It's not for safety or security after all, but just to keep people from walking in on you while you're sitting on the toilet or whatnot.  So I explained to Harriet that she'd locked the door, and asked her if she could turn the handle on the inside (more giggling), then said I was going to get a tool to open in.  Returning with a long thin screwdriver, I confidently inserted it into the thin hole... and hit wood. No hole to the other side of the door.  No way to pop the lock.

Before this morning, I didn't even realize that the old-school doorknobs on our upstairs bedroom even had the ability to be locked.  But honestly, the fact that Harriet has discovered it did not surprise me.  She's very good at noticing things that are unusual or out of place, and spends a lot of time trying to figure out and understand the way that things in her environment work.  In fact, just last night she delighted both my wife and myself with a new inquisitive question.  Her bedroom story the past few nights has been a documentary on the Soviet N1 Moon rocket, since rockets are a big thing for her right now, more exciting even than dinosaurs or airplanes.  
Harriet, playing "Rocket toddler" with my father.  First, you stand on your "launch pad" while the grown-up does a count down...
...then the grown-up yells "whoosh" and lifts you high in the air while you scream in delight.
As we finished the documentary last night, she popped out: "How'd they do that?" and we were hooked by her inquisitiveness---we're really suckers for questions from our daughter.  I said we'd look and see, and there on the "related videos" bar was an episode of a show called "How Hard Can It Be?" in which three engineers spent a couple of weeks trying to send a home-made rocket into space.  We watched it together, with commentary, and she was fascinated with every moment---unlike the moon rocket documentary, which made a good bedtime story because it interspersed occasional exciting blast-off shots with long boring periods of old Russian and American engineers telling their old engineering stories.  And so it's no surprise that Harriet found a way to lock her parents out of her room that they were not yet even aware about.  And yet there I was, still locked on the other side of her door.

Well then, I told my daughter that she's done a very good job locking me out of the room, keeping my voice light and playful even as I'm starting to worry in the back of my head.  Playful giggles and taunts from the other side.  But I now know that I'm working with a toddler time-bomb on the other side of the door: she's up because she's hungry and she wants out, and if she starts to get upset while I'm locked out of the room, then we could have a serious crisis on our hands.  So I start bringing more tools up, all the while keeping up a conversation with a toddler who's decided that all this is a lovely game.  The screws come out, and the handle won't come off.  The door is too well sealed for me to exploit my old breaking and entering skills from the days when I did urban spelunking (a story for another time) and slip a card around to pull the latch in directly.  All of which ended up meaning it was time for me to have another new experience.
"OK, Harriet, I need you to step back from the door."
"OK, Daddy."
"Are you standing away from the door, little one?"
"Away from a door."
I hope.  I hope she means it and isn't just repeating what I say right now.  I crunch my hip hard against the door, right by the knob to try to do it right and minimize the damage.  High pitched and excited laughter from inside the room.  I crunch a couple more times, pushing and pulling at the same time to keep the door from popping open fast, and the door jamb breaks and lets me in. The milk I've got with me, poured into her favorite cup in anticipation of this moment, goes straight into her hand, and I praise her and make light of things, and she stares at the fascinating new mess I've made.  

A few minutes later we're downstairs at breakfast, and I'm burning off adrenaline by making pancakes and teaching her the MIT Engineer's drinking song, doggereling as I go to try to avoid all of the drinking, sex, and cursing (which is rather difficult).  And when I tell her that after breakfast I'm going to try to fix her door, she asks me that wonderful question once again: "How'd they do that?" 

So after breakfast, we went back up to the door together. I explained how the lock worked to her fascinated eyes, and she oscillated back and forth between playing on her own and watching me take apart and repair the door (the jamb is... serviceable, and next time it will be possible to unlock the knob from the outside as it should be).  Harriet made drill sounds to help me out, and told me a story about a hungry lion to keep me company, and in the end all was right in the world again.

And so, in sum, the unexpected things that I have learned this morning:
  1. Harriet is now capable of rather sophisticated mechanical activities, and given her curiosity about what things do and how they work, it's only matter of time before she starts disassembling our appliances.
  2. It's actually much easier to break a door down than I had realized previously.
  3. The Engineers' drinking song really desperately needs a clean version that a kid can sing.

Sunday, August 10, 2014

A Football Team of Moose

The first stuffed animal that I ever received as a child was a moose, hand-made by my parents' friends Joe and Suzanne Stupak, who lived up in Maine and gave the moose in token of the Great State to the child of their friends in Massachusetts.  I was about six months old, and have no memory of receiving it, but I named him "Oom-pa-pa" and grew up with him thereafter.  One of my earliest memories is from being three or four years old, in bed and realizing that I didn't have my precious moose with me, and running (unsupervised) out into the back yard to find him where I had left him, lying out in the moonlight with his marble eye reflecting back whitely in the glow from the sky.

When I was in kindergarten, we moved to Maine, and moose began to grow in importance.  My first was joined by Big Moose (who was big enough for me to use as a pillow) and Jay Moose (who I hollowed out into a puppet when he began to lose his stuffing), Sister Moose and Mama Moose (whose antlers I cut off, because female moose don't have them), Bruce Moose and Spruce Moose and Eric Moose and more. Every Christmas, I got a moose, and every birthday, I got a moose.  For a while, these totem animals were all-important outlets for my less acceptable forms of behavior.  Moose were stupid and big and happy and uninhibited.  They were impervious to harm and absolutely impossible for any adult to ever control: they were elemental forces of human nature.  Moose could eat lots of beans and fart.  Moose were able to attack my little brother.  Moose would yell at the top of their lungs and knock things over and any other rude thing besides.  In my elementary school drawings, one finds moose flying planes covered in piles of crazy weapons, first blowing up Communists and later locked in their eternal war that developed with my Lego people.  Moose were the Id, just acting and destroying as they needed and desired, while the Legos were a creative force, building huge and complicated cities.  My parents managed this as best they could, balancing freedom for their child's imagination with attempts to eventually civilize the little beast.  Perhaps indicative: our old family rulebook includes an agreement that bans moose from the table, except during certain special occasions such as Christmas morning and birthdays.

As I grew up, though, the need for moose to be my outlet waned, of course.  I made more friends, discovered roleplaying games, and generally slowly shifted from the simple joys of early childhood to the more complicated forms of make-believe that made me happy in adolescence.  Of course the moose were kept around, and I still used big ones as pillows on my bed.  And still the tradition of gifts continued, my family still giving me the moose of tradition and custom, and various other relatives noticing "Jake's into moose" and giving me moose-themed things as well.  It's not a thing I ever objected to of course, even as I grew disenchanted and uninterested: these gifts still called back to times when moose still mattered more, and the sentiment and love they came in mattered even if the creatures didn't.  But they stopped getting names and the new ones no longer had a chance to start developing personalities of their own.  They just accumulated on my shelves, a pile of animals that would have been better gifts for younger me.  But give them up?  Of course not: even if I no longer played with them, the moose would always evoke those days I did, and the times of joy and wonder when it all was new.

By college, I'm not even sure if any moose came with me.  I think that probably yes one did, but wasn't one that was the most important and would have sat neglected on a shelf.  A few more came at holidays, but quietly and with mutual consent, the influx stopped and the moose stayed up in Maine, shifting eventually from my bedroom into storage space in one of my parents various stages of house renewal and renovation.  And there they sat.  For me, it was important that they still existed, but it wasn't important to actually see or interact with them.  My parents, though, would occasionally ask for me to take them off their hands.  And so, when the papers came down this summer, so too came two good-sized garbage bags full of moose, the result of twenty years of slow accumulation.

I sorted them, is what I did.  In one sealed plastic box went the moose that I had emotional attachment to, to go out West to Iowa and a new basement for them to season in, and see if ever there came a time for them to either go upstairs or go away.  The others, whose names I did not know, plus a couple of freaky or otherwise distasteful known offenders, went into a bag to await delivery to Goodwill.  It might have ended there, of course, but I was not in a hurry to get them there, and so they sat.  And Ananya, thinking of my words about wanting to share some things of mine with Harriet, brought her in one day while I was out, and let her pick a favorite from the bag.

Harriet has a very different relationship to stuffed toys than I did, so far.  I had very few when I was small, and so each toy became an alter ego, with a very strong and individual personality.  Harriet was inundated with stuffed toys as a tiny infant, as many different people each carefully and thoughtfully picked a meaningful gift that happened to be from the same general category of things.  As she's grown then, so far her animals tend to instead have more contextual personalities.  Seal is for sleeping, and Bagh and Khargosh are safety animals, the wonky musical Giraffe is for giggling with, and so on and so forth for various different ones.  Moose, her new one, is an adventure animal.  Moose wears bright red Indian dresses and dances, along with the boots that don't fit Harriet any more, and goes out on rides and plays in more exciting ways.

And then... I was packing, and thinking about that great big bag of moose that had not yet gone off to Goodwill.  Harriet was up there with us, playing with boxes and stickers, and I thought: why not see?  Let's see if any other moose were ones that she would like to keep.  I pulled the bag out and let her start to sort on through it.  And she pulled all of them out.  Well, of course she did.  And she's much more interested in the new, unloved ones than in the old and scruffy moose of back in my earliest days.  But this relationship is very different.  So far at least, for her the moose don't come as individuals but as a pack---Ananya likes to describe it as "the moose are a football team." And she plays with them in big piles, as you can see:
Harriet, in a great big basket of Moose
I carried her up and down the stairs, and pushed the basket at her request, so the moose-car and its driver could go vrooming all around the room.  It's not my way, but it's not my play, and in this unexpected passing of the generations, the moose have all won their reprieve from Goodwill (except the couple of creepy ones, who I denied appeal summarily to).

Saturday, August 02, 2014

Psalm 6.111

Following on my recent theme of things past and rediscovered, I wish to present to you, dear readers, a recently rediscovered poem.  To give some context: I wrote this in the fall of my sophomore year at MIT, in the midst of taking the digital electronics lab course, also known, in the MIT penchant for never using a name when a number will do, as 6.111, or sometimes more affectionately as "Digital Death Lab."  This was the time when many of us became quite intimately acquainted with the workings of a good oscilloscope, when one stayed up wiring breadboards by hand late into the night, comparing the neatness of ones wires with the friends who were doing the same.  This was the time when we learned that "digital" only really meant digital if you didn't drive too many circuits with your output, or mix high frequency signal lines, and if your power supply was clean, and a hundred other things that are the whole point of getting kids frustrated in a lab class: "In theory, there is no difference between theory and practice. But, in practice, there is."

At some stage of progressive insanity, the first line of this poem mutated into my head from its origin in Psalm 23, and it then became a thing that was absolutely necessary for me to write and distribute to others, and my friends and I did so anonymously.  They might have helped write and edit some too---at this remove I have no real recollection, except for remembering a feeling of inspiration, and then of company in its execution.  As for you, dear readers... well, I suspect that some of you will get it and some of you will find it only mystifying, and really that's OK with me.  And so, without further ado...
Psalm 6.111 
Some words of comfort for the days ahead: 
The FLIPFLOP is my Synchronizer, I shall not want.
He maketh me to pipeline my whole circuit,
He leads me to program more EPROMs,
He restores my sanity.
He guides me in paths of synchronicity for his clock's sake.
And lo, though I walk through the valley of the shadow of CMOS,
I will fear no intermediate voltages,
for He is gated, His one or His zero, they comfort me. 
You prepare a haven for me in the presence of metastability.
You anoint my design with blocks, my logic shall rationalize.
Surely good grades and sleep will follow me, all the days of this semester
and I'll not dwell in the room of the LAB forever.

Thursday, July 31, 2014

Naming, branding, and the temptations of mediocre acronyms

Naming things is easy.  Naming things well is hard.  As both an American and a scientist, I have a strong affinity for acronymic names, and they litter my work.  MADV, TASBE, PACEM, SBOL, CRF-gradient, AML, CRP, they breed and multiply in every project, because it's easier than coming up with a new but pseudo-meaningful word.  If you're striving for mediocrity, as I often do in project titles, then the acronym generation game is easy.  I play it in three steps:
  1. Write down a bunch of words vaguely associated with the project.
  2. Scrabble their first letters to get words or word-ish sequences that are at least pronounceable.
  3. Try to ensure that the sequence of words is at least not objectionable.
And that's how we end up with a name like PACEM (Proto / Amorphous Collective Energy Management) or TASBE (a Toolchain to Accelerate Synthetic Biology Engineering).  But honestly, those are just not terribly good names, because I don't have a natural knack for branding and I haven't ever really invested in it.  Now "Scrabble", that's a name that I can really get behind: it really conveys the scrambling and shuffling that goes on when you play the game, but doesn't go acronymic to take the lazy way out.

Naming is on my mind today, because we've been doing a huge overhaul of our Proto programming framework this summer, and since the programming language that comes out of this will look very little like Proto currently does (for those who care, it will switch from prefix to infix notation and all those LISP-ish parentheses will go away) we might take the opportunity to coin a new name.  So we've been kicking around ideas and trying to get away from the acronym thing.

It's really tempting to get cute when you're naming things, and in my experience this always will tend to end badly.  The problem is that once you make a name, you get stuck with it.  A joke is nice, but do you really want it pinned on your lapel for a decade of your career?  Or worse, a joke can end up with you not able to be found at all, because you get lost in the noise or incomprehension.  Though, perhaps not always... I had an undergraduate working for me some years ago, who came up with an extremely fast and elegant algorithm for accelerating complex chemical simulations.  When we were nearly done writing it up, I told him that this algorithm needed to have a name, and he asked me, "What are the rules for naming algorithms?  Can I name it anything I want?"  Incautiously, I told him yes, having apparently forgotten the madness of power that would have overtaken me at these words when I too was an undergrad.  

And so it is that I came to be coauthor on a paper about the LOLCAT method for chemical simulations.  I could have quashed it and demanded we have a better name, of course, but he was so happy with the idea and it was really mostly his invention, and so I gave in and we've got this crazy name.  It's not even an acronym with some sort of reasonable excuse, it's just LOLCAT because my undergrad was mad with power and hilarity, and I was quite content to let him have his fun.  If you google LOLCAT, well... either you already know, or you should do it now.  If you google "LOLCAT algorithm," though, we come up on top, and (I just discovered) it's even apparently gotten me into Wikipedia.  So I guess that means that names don't matter too much after all, if you've got something useful that you've built, in the end.

I'll definitely say, though, that there's one thing I'm very proud of in my history of naming: Harriet (seen here in her mother's lap, watching airplanes landing over her into Logan)
That name was subject to extremely careful thought, since a person would be branded with it for her whole life (or at least until she gets old enough to change it legally if she chooses).  It came to me one night about halfway through my wife's pregnancy, as I was biking across town and tumbling around my thoughts on naming constraints: instantly recognizable but not too common, no strong cultural baggage from famous people or stereotypes, needs to have good "weight" on the tongue, something that can enable a strong woman to choose whoever she wants to be when she grows up and not get in the way of her being taken seriously.  So far, it seems, that Harriet has fit the bill, and she wears it proudly, along with her Indian middle name, Purna.  We'll see which one she settles on as she grows... 

Friday, July 25, 2014

Down-Time Brain

I have the impression, sometimes, that I used to be able to work much harder than I do these days. Like, that I would stay up all night coding (which I did sometimes) or that I could squeeze productive work into any little crevice of time.  And sometimes, that was certainly true: I definitely remember times when I would take a single free hour between classes and zip over to find a computer to churn out a character sheet, or set down in an alcove to do some math or something. I look at that today, and wonder why it's so much harder for me to do that than it used to be.  I also, however, look back and see that there were so many times where also I didn't do that.  Like when I would go to the back of the science fiction library at MIT and pull down books and curl up on a chair that used to be there in a corner to read for hours, or just hang out and shoot pool or watch movies.  In early grad school, I would come home and my roommate Won & I would crack jokes while watching Cartoon Network and Sci-Fi channel shows for hours---we never missed Sealab 2021 if we could help it.  I somehow felt very productive and focused and also had a lot of time to spare.

Today, that is not so, I think.  It also, though, might be that it is more a shift of attitude.  And also, of course, responsibilities.  The entropy levels I live with are much higher, and my tolerance for entropy has definitely gone down from undergrad.  My god, but summers in our house were awful.  I lived, in my undergrad years, across the Charles river at one of the many MIT fraternities strangely stranded on the other side, in Boston.  Because there were always things to do, I never went home for the summer, but stayed to work on one scientific project or another.  A lot of people did that at MIT, and I enjoyed it.  Except, of course, for the horrible smells.  During the school year, our house got cleaned on a weekly basis---by freshmen in the Fall, and as part of a rotating schedule of duties in the Spring---so even with thirty undergrad guys and various associated others, things never really got too bad.  The summer, though, although in theory there was a schedule, it simply wasn't enforced and things built up.  I remember quite viscerally the day that I walked into the kitchen and noticed little white grains of rice all over the floor.  Thinking nothing of it (it was summer after all), I went to the fridge and got my breakfast out: canned peaches and refried beans, each served cold from a SysCo commercial #10 can (senseless undergrad, remember?).  As I turned to leave, I noticed the grains of rice were moving, slowly.  And then I realized that it wasn't grains of rice at all, but a remarkably large number of maggots, all moving radially outward from the overflowing can of trash.  This was my first encounter with a real live maggot, and you know, although I was horrified and disgusted, I didn't either attempt to clean it up or even think to tell anyone about it.

These days, I can't imagine that I could let such nasty horrors go.  Just an hour earlier this evening, I took a barely started bag of trash outside because I couldn't stand the diaper in it.  I get a serene and satisfied feeling from having a sink that's clean and all toys put away to have a clear and empty floor.  Indeed, I only lightly resent the duty.  And that's a thing that takes my time.  And parenthood, and maintaining our house, and just the daily fight against oncoming entropy.  I'm always tempted to short my sleep, to try to find more time for my work, and sometimes I do it for weeks on end.  But then, I think it's not a really long term plan.

In truth, however, I think I'm quite productive, those times that I'm not feeling down on myself.  A major difference from then to now is also the amount of things I juggle.  And no, I don't think I'll get into that and try to do some sort of bragging enumeration.  My wife and I have recently made a deal that we won't list deadlines at each other, when talking about our stress or planning.  We just should always assume that we are both likely under the gun on something.  I feel that when we talked about it, it always was a spiral down.  I much prefer my down-time brain, those times when I can actually just let go and not stress out about the things to do.

I'll never be stress-free, I think.  When life is empty, I have filled it with new commitments, projects just for me and my enjoyment.  And when it's time to play, I should just play.  Snuggle down and watch a good-bad guilty pleasure movie, my wife and daughter snuggled up with me, like we did tonight.  Let my head roam and see what thoughts will come.  I had a good week and lots of things got done.  Perhaps I'll share some other time.  For now, I think I'll settle down, and not let myself get worried too much.  The time for that will always come.

Sunday, July 20, 2014

Requiem for a Ray-Gun

This summer has seen a lot of time for nostalgia for me, and one of the big sources has been going through the old papers that my parents passed to me at the beginning of summer.  They're preparing for downsizing, and finally made good on the request / threat / reasonable-demand that I take all the remaining boxes of my old stuff off of their hands.  Since we're back in Boston for the summer, it was easy enough for them (relatively speaking) to pass on a carload of bankers' boxes as a side effect of one of their trips down to visit, and thus give me custody of things I probably should really have dealt with long ago.  And so it is that I've had a while going through twenty-year old boxes and unearthing some remarkable reminders of who I was as a youth.  And sometimes also, who I still am, to an uncomfortable degree of accuracy.

Interestingly to me, the earlier that I go in my education, the higher a percentage of the papers I find worth saving.  From grad school, I basically threw everything into the trash.  Undergrad, a few things survived.  High school yielded a great deal of fascinating essays and uncomfortable personal truths, but also a lot of translated Latin and math problems to simply be discarded.  Pretty much anything from earlier that had survived was still worth keeping.  Some of it, I think, is that my parents only held on to the memorable things from back when they were making decisions: there are no piles of practice sheets drawing letters of the alphabet, nor are there the arithmetic quizzes that my fourth grade classmates and I used to race each other to completion on.  Once we hit my own eras of curation, the pre-filtering has not yet happened.  Another and more important thing, however, is that as I grew older and my education became more specialized, my own set of life choices have tended to dictate that the classwork is more technical and less creative.  Reading essays and stories that I wrote in high school is like taking an archaeological core sample of my personality and history.  Reading algebra notes is just reading algebra notes that could have been taken by anyone.  Although, as I think about it, I'm sure that a lot of other people took more interesting notes than me, putting little cartoons or editorials about their feelings on the material in.  I just wrote it down and never once looked back to read it, except in unusual circumstances.  And having saved class material that is essentially just a poorly transcribed technical manual, why on earth should I hold onto it?  Either I use it every day and I know it still, or I have forgotten it and will re-learn the knowledge from some online source when I find a need.  My creative output shifted out of the classroom and into other areas, and by the time that I reach grad school, you can see my records in the early papers and screeds on my website.  There are times when I am tempted to purge the earlier and more embarrassing of these, but so far I have resisted.  I feel like it's something I need to just be honest and live with, even if some of the memories associated with those papers are ones I think that I would just prefer to forget.  And why, oh why, do people cite them?  I can only assume that they have found things more valuable in certain of them than I the author know in retrospect.

The motivating artifact for this post, however, was not a school paper, but one of the halo of other related objects that I found in those boxes.  You see, back in high school, my little nerd clique and I were all involved in writing computer games, and managed to compete each other into something approaching real competence.  We released a few games that were pretty awesome for our egos and tried to get serious and make bigger and better and more significant contributions.  One place that we over-reached was getting into 3D.  Oh, it worked and all, but despite our wishes we just weren't quite Bungie and couldn't aspire to match our engine to our idol Marathon.  But we put together a working engine that ran at a decent frame rate and started building worlds and enemies and such.  And here is where my ray-gun comes from:
Rather than try to draw the art that we were nowhere near capable of, we did a photo shoot with the fancy new "digital camera" thing my brother's friend Jeff had.  We set up a studio in one of the rooms of our house (now a guest room, but I think it was my mother's art studio at the time), used a white sheet as a "green screen", and got into costumes with the awesomest future bad-guy gear that we could come up with.  I wore a green SWAT-team outfit left over from playing a garbage man in a school musical (it was an odd show), carried a shotgun we'd borrowed from somebody, and scowled beneath the darkest aviator shades I could lay my hands on.  My brother wore hockey padding and a hockey mask and carried the ray-gun above (in the game, it shot energy rings at you).  Jeff wore the same hockey gear and a handheld small vacuum cleaner strapped upside down to his back, holding the straight steel tube out as the business end of his "flame thrower."  We shot from all angles, getting walking animations, attacks, injuries, and deaths.  Some PhotoShop time on the secondhand probably-legal copy I'd gotten my hands on, and we had glorious, glorious enemies that made everybody laugh at us because they knew who was trying to look badass under those shades.

It was great fun, and we got a long way, but the game never finished and never got released.  I'd wander around "debugging" by shooting myself and finding geometry problems that had to be addressed.  Our ambitions grew bigger and we kept trying to get a better engine and tell this giant story that was trying to brew, but none of us had read The Mythical Man-Month yet and we never just stopped at "good enough" and finished a game of some sort.  I moved on to another project, then college, and our software-making club dispersed as everybody else did the same. By now, the images are all long gone, dead long ago on obsolete media and obsolete computers.

The ray-gun, though, was waiting for me, coming up slightly dusty and otherwise good as new from one of the many boxes of archival stuff.  Showing it to my wife, I fired it, just to see.  The staple shot out and bounced pinging off a wall into nowhere, and then I needed to scramble and find it so it wouldn't pose a toddler hazard.  The ray-gun didn't get a decision that day.  Instead I put it off, and shoved it high on top a bookcase where Harriet would never see it, let alone get to test whether she could injure herself with either staple-gun or pneumatic door-closer.

I looked again up there today, and took it down to disassemble.  The choice was obvious, but bittersweet.  I just don't need this artifact: all that it can be is a trap for an unwary child some day to discover.  What I care about is the memory, to know this wonderful ray-gun once existed, made for a hot summer day in a makeshift studio in an appropriated third-floor room, where half a dozen kids dreamed of fame and fortune and dystopian future storm-troopers.  Remembering all of this, I laid the ray-gun on a black towel (shades of its earlier backdrop) and snapped photos until I had one I was satisfied could be enough for memory.  Then off came the packing tape securing the two halves together, and the gun was gone.  The old door closer went into the trash; the staple gun will join my tools, and will in time no doubt be put to its old and original use.  But if it's me that uses it, I guarantee that every time I fix a staple, a part of me instead will want to stop and wave it around in the air making ray-gun sounds: "P-tanngg! P-tanngg!"

Saturday, July 19, 2014

Notes from The Princess Invasion

Having just been (very) rudely awakened by a toddler, I'm lying here all sleepy but not quite sleepy enough to go back to sleep apparently.  And so, it seems, I am finally breaking my long pause in blog posting.  I don't think I'll bother writing about not posting right now---that kind of post is something I feel is generally not too interesting to read, and besides I don't have any particularly interesting reason that posting has not been happening.

Instead, I think that I will tell you about our Princess Invasion.

It was, I think, a fairly inevitable thing.  Harriet has just turned two years old (her party is today), and despite our failure to expose her willfully to lots of Disney stuff, it's out there and it comes for little girls.  Nothing, I know, is new in what I'm saying.  My sister-in-law shared a book called "Cinderella Ate My Daughter" a while back, about the ubiquity of princesses and pink in the mass culture that we live in.  It's out there, it's going to come for them, especially through peers and daycare, where even the most controlling parent cannot isolate, and all we get to do is choose which ways we will and won't react, and try to navigate through as best we can.

Still, I think it was an ugly surprise when it appeared so suddenly.  My wife told me of the moment just two days ago: she'd been putting Harriet in the car in the morning to go to daycare, and our little two-year-old did not want to be buckled in.  Not being an area where compromise can happen, a struggle ensued, and after our little small one's inevitable loss, she registered her final protest: "No! I am a PRINCESS!"  Command, and dignity.  The penetrating hauteur of one who knows that she must be obeyed.  We're trying not to laugh too hard.

That night, we took her out to a toy store to get a bicycle/tricycle, so that she could pick her own out.  We like to give her choice and options when we can, and just try not to wince too much at what she picks.  We now have a lovely lavender tricycle in the house with pictures of a girl doctor who invites us to help her solve mysteries when Harriet pushes buttons.  But also, we found this:

In case you can't quite tell, this is a bright pink toddler chair with a heart-shaped back, covered with Disney princesses.  I didn't even recognize them all any more---having just looked them up, I can tell you that the black princess on the arm is apparently Tiana, from a retelling of the frog prince, and the left-hand blond on the heart is Aurora from Sleeping Beauty.  Front and center, of course, is Cinderella, and we also have Ariel, who radically alters her body in pursuit of her prince, Belle, the role model for abusive relationships, and Snow White, the Disney ur-Princess.

The moment she saw this chair, Harriet hopped off her bike and beelined for it, picking it out of all the other options.  No, it didn't come home with us.  But as long as we were in the store, our little princess could have her pink chair time and celebrate her royal company, and so she did with great delight as you can see, and great velocity and vibration, which doesn't come through as well in still shots.

I am an American with a daughter.  We're just going to have to deal with this.  And so far, at least, it's not all one way on the gender coding, which I think is also a good sign.  Yes, she's wearing Batman shoes.  She likes those too, and they aren't pink.