Half Awake

Last month I attended a computational science conference in Washington D.C. The organizers of this particular conference are big into helping the students who attend make connections in town. To this end, they try to set up meetings between the students and congressional staffers from our home or school districts. In some cases we’re ever able to meet the congress members themselves.

Somehow they manged to cram me into three meetings into a single afternoon, and I found myself getting blisters on top of blisters hiking circles around the Capitol complex to meet with staffers in the offices of Rep. Barney Frank (MA), Senator John Kerry (MA), and Rep. Maurice Hinchey (NY). Meeting staffers can feel awkward and frustrating, particularly if you don’t have an agenda. Even if you do have an agenda, you might not get more than “The representative is a strong supporter of all the issues you mentioned.” I might write more about my strategy for these meetings later. For now, I want to talk about a particular comment that came up in Senator Kerry’s office.

A group of four graduate students had been scheduled to meet with one of Senator Kerry’s Legislative Correspondents, Lindsay Ross. Ms. Ross was actually the most engaged staffer I’ve met on Capitol Hill. She showed genuine interest in meeting us and learning what issues were important to us. At one point, the Energy Bill and energy technology came up, and one of my peers offered this challenge to the staffer:

There was a time when communication was what limited progress in this country. Back then, we invested in information technology, and now communication is free. It’s totally revolutionized the way the world works. What if we invested in energy in the same way? Can you take a moment, and just imagine a world where energy was free? <dramatic pause>

-Some Guy, Washington D.C.

I can imagine such a world, and it frightens the CO₂ out of me. A world with infinite energy would have infinite consumption. For the first time in decades, Americans are (ever so slightly) curtailing their consumption of petroleum products. Even those who aren’t cutting back seem to at least be paying attention. And how can you not pay attention with daily messages like these? But if energy were suddenly “free”, there’d be a huge rebound effect, with disastorous consequences for waste, pollution, and climate change.

What frustrated me the most was that Ms. Ross had stars in her eyes after this guy’s diatribe. In D.C., everything about solving the energy crisis seems to center around sustaining an unsustainable system. I know that the person who said this has his heart in the right place. His goal was to push for funding into new and more renewable sources of energy, which could have a good effect. I just wish that he’d said “Can you imagine a world where energy was clean and renewable” instead of bringing it back to energy cost, and therefore consumption, so quickly.

I am terrified by this story, not to mention the inevitable backlash (from both pro-life and pro-choice groups) that it will create. I saw the story at Feministe, and a couple of the commenters there are convinced that it’s a hoax, but the Telegraph in the UK has already picked it up, and it seems to be gaining momentum rapidly elsewhere. I don’t know if what the student did in her project is medically feasible, and it sounds like she offered little supporting evidence (I do not suspect she is expected to provide such evidence for an art project, particularly for one as private as this).

Update: This has been reported to be a piece of performance art (i.e. hoax) by the Yale Office of Public Affairs. From the website:

Statement by Helaine S. Klasky — Yale University, Spokesperson
New Haven, Conn. — April 17, 2008

Ms. Shvarts is engaged in performance art. Her art project includes visual representations, a press release and other narrative materials. She stated to three senior Yale University officials today, including two deans, that she did not impregnate herself and that she did not induce any miscarriages. The entire project is an art piece, a creative fiction designed to draw attention to the ambiguity surrounding form and function of a woman’s body.

She is an artist and has the right to express herself through performance art.

Had these acts been real, they would have violated basic ethical standards and raised serious mental and physical health concerns.

Phew.

Update (4/18): A new post on the Yale Daily News site quotes Shvarts (the artist) saying that the university misrepresented her. From the piece:

But Shvarts reiterated Thursday that she repeatedly use a needleless syringe to insert semen into herself. At the end of her menstrual cycle, she took abortifacient herbs to induce bleeding, she said. She said she does not know whether or not she was ever pregnant.

“No one can say with 100-percent certainty that anything in the piece did or did not happen,” Shvarts said, “because the nature of the piece is that it did not consist of certainties.”

So now we’re back to a more disturbing, yet more ambiguous, scenario.

Update (4/21): There’s an interesting series of statements from the Yale Office of public affairs.  Apparently the administration wants a more unambiguous statement of what went into the project if the student is going to present it.  I think this is a good move.  Shvarts wants to provoke discussion, and I see value in that, but right now nobody knows exactly what they should be discussing, nor will they unless she settles down on exactly what her project entailed.

Here are a couple of the photos from the breakfast I mentioned.

More recently, our class had a media training workshop where we practiced constructing clear messages, using sound bites, and performing camera interviews. It’s sort of terrifying to be on camera speaking as an ‘expert’ about something that in reality you don’t feel that confident about.

We watched a number of examples of good and bad interviews. One excellent example of what not to do came from an interview of Bob Dole by Katie Couric during the 1996 presidential election (sorry, I can’t find a video of it). Dole was downright combative rather than focusing on the issues that were important to him. But it’s tough. I’d probably blow up at a reporter who accused me of anything, too.

I think I could do a good job as the journalist too, though. I like asking questions and being critical of the responses (in a constructive way, of course). I like listening. Maybe there’s a career in sci-comm or policy for me after all.

This morning my science communication class had breakfast with Mr. William Nye. We sat in a small classroom and for the most part, he spent the time asking us questions about what we do and why we’re in the class. When he got to me, and I explained my research on the minimal gene set (the smallest possible set of genes that can still support bacterial life), he asked me how large such a set would be. I said something like “well, we know there are bacterial species that have around 400 genes, so the smallest set is obviously smaller than that.” Bill called me out for that, firing back “it’s not obvious!!” He was just kidding around, but it was a good reminder that I shouldn’t use presumptive language when describing science.

It was impressive how kind and engaged Bill Nye is. As soon as he got to breakfast, he immediately hugged the instructor of our class, and another student in the class who he recognized. He really strikes me as a genuinely caring individual, who got into his business because he wanted to talk to people about important problems. Definitely an inspiration for how I’d like to behave as a scientist.

Note: I was holding off on this post because I wanted to post some pictures from the breakfast, but I haven’t gotten them yet. I’ll try to get them up in the next couple days.

A few days ago I wrote about some blogging tips I had gleaned from a talk by Ancient Wisdom Productions. I alluded to what some of my reasons for blogging have been, though that wasn’t exactly the reason for the post.

Today I saw a video of Clive Thompson talking about why he blogs (link via Baxt), and I think I have a lot in common with his motivation. As Clive explains:

I do it to sort of record stuff that I’m interested in, that I see, what I think about it. It helps me like literally think ideas out… I know [a concept] intrigues me, I don’t know why. As I write the blog entry, I literally develop the thoughts. So it’s a way of developing my thoughts, and recording them, so that you know, months later, I can look back and remember, and re-experience the stuff that I was interested in.

The focus of the interview was science and technology blogging, but I think the same reasons are broadly applicable. He also touches on the important aspect of user feedback, and reminds us that if you don’t want to blog, you don’t have to.

The Inbox Zero Google Talk recently inspired me to get my research life organized. E-mail organization was a logical place to start, and my desire to try to keep a low number of messages in my e-mail inbox was easily adaptable to the “process down to zero” method promoted by Inbox Zero.

Now I’ve moved on to research papers. For the last several years, I have collected papers in various places (PDFs in a references file, printouts all over the place). When I actually need to organize these for some reason (i.e., to write a paper), I typically go and download all the citations into either Endnote or Jabref, and then assign each paper a unique 5-digit ID number. Then, I put that ID number in the ‘label’ field in Endnote, and keep the PDFs and papers sorted by ID number in my computer and/or filing cabinet.

This system is great for finding things fast, as long as I know what I’m looking for. However, if I want a number of papers on a particular topic (let’s say, ’synthetic biology’), I either need to do some searching within Endnote (which can be hit-or-miss), or I have to know by memory who wrote the papers on a particular topic, search for those authors in Endnote, and then retrieve the papers by their 5-digit ID number (my memory doesn’t do well at this).

In the end, I duplicate a lot of effort in finding papers that I’ve already “found”.

I’ve done a bit of googling on this topic, but nothing convincing has come up. The best resource I’ve found was at Ask Metafilter, and it’s pretty weak. Some of the possibilities I’m considering are:

• File by category - This works well for quickly finding a set of papers on a particular topic, but it can fail when one paper belongs in multiple categories (either you won’t find it in the folder where you think it should be, or you will have multiple copies of papers in your file).
• File by author - This has a lot of the same drawbacks as filing by ID number, but the added advantage of forcing you to think more about who writes what, and becoming more familiar with their names.
• File everything electronically - This scares me, because I still prefer reading papers on paper. However, it would greatly simplify the storage and searching process. How bad is it for the environment if I just print a paper every time I need to see it?

If you are faced with the same problem, or a similar one, I’m curious to hear how you handle it. I know no system will work for everyone, but I’d love to try something that simplifies and streamlines the process. I’m also interested in comments about particular software or processing steps that you like.

A little less than a year and a half ago, I decided to start a blog so that people I know could have a small window looking out over the events of my life, and so that people I don’t know could have the chance to cut me down for expressing my thoughts on the internet.  Really, I started it on a whim.  I thought that writing about nothing and everything might help me feel better about the parts of my life with which I wasn’t totally happy.  And I think it did partially serve that purpose.  Expressing my thoughts in a place outside my head seems to engage a different, underused, part of my brain, and that’s been cathartic.  I still blog for those reasons, but the focus and applicability has been expanded.

Today’s topic in the Science Communication Workshop that I’m taking was “Web Media and Making Your Research Homepage/Blog”. Most of the discussion revolved around blogs, why one might be interested in reading blogs, and how/why one might write a blog.  Bruce, the instructor, gave us a primer on blogging, and we were also treated to a blog design presentation from Molly, Tyler, and Casey of Ancient Wisdom Productions.  I came away with a renewed enthusiasm for blogging, and a list of useful tips from the AWP reps:

• “Design matters” - This was definitely the focus of the AWP talk, but probably the part I will think about the least.  What font we should use.  What line spacing we should use.  How the colors we choose should contrast.  Information hierarchy. It’s a lot, and I really do truly believe that it matters. However, I’m probably going to ignore anything that WordPress takes care of for me (for now, anyways). Someday I hope to be able to pay someone lots of money to make my ideas look pretty.
• “It’s All About Content”- They recommended blogging a lot, at least once post per day if you want to keep people reading.  This makes sense - I know I am much more likely to come back to blogs that update regularly.  Some blogs seem to update too frequently (this is an arbitrary descriptor, and depends on mood, interest, and attention span).  For example, I (personally) couldn’t keep up with the frequency and length of posts at Dooce, so I had to remove it from my RSS feed (I still browse over there manually though). 
• “Don’t Be Afraid to Swear”- This one reminds me of a post I’ve been meaning to write about swearing, but I think the take home point is that blogs do well when they have some character. 
• “Blog for the Moment”- They explained that most people judge a blog by what’s in the most recent posts, and that digging through the archives is relatively rare.  This may be true, but I also know that most traffic that comes to this blog is via keywords that have only appeared in single posts in the archives.  I wish I had a better idea if that traffic ends up visiting the “home” link.
• “Tag the F out of your posts”- After the presentation I asked what their recommendation for tagging and categories was.  They said they liked to have a limited list of post categories, with no more than one category per post.  At the same time, they recommended adding as many one-word tags as you can think of.  Now that WordPress has actually separated tags and categories, this is doable and also sort of fun. 

One of the most interesting impressions I gleaned from the session was that a significant portion of the class is quite anti-blogging.  They think that most blogs are junk, and that the comments are even worse.  They might be right, but I disagree with their (apparent) conclusion that the junk makes blogging less worthwhile. 

First and foremost, our goal in this course is to communicate science to everyone (or at least, to as many people as possible).  That includes the people writing, reading, and commenting on junk blogs.  Communicators of science will almost certainly have to explain ideas to people who don’t get it, don’t care, or just aren’t nice, but whose opinions still matter.  I think blogging is good practice for this.

Secondly, the junk can be amusing.  Read stupid comments.  Respond to peoples’ nonsense.  Get in an argument with someone you don’t know and will never meet.  But, to quote Wil Wheaton, “Don’t be a dick!”.

Fracas’s sequel to her award winning story reminds me that it’s been a year since I placed in the same contest with a post proposing a blog focused on Inquiry Based Learning in Systems Biology.

My blogging has ended up being a lot less about science than I had originally intended. I thought I’d write more about my own research, but feel that I never have anything to say about it. I thought I’d read cool articles and post summaries here, but I have enough trouble reading them without having to write about them. Needless to say, I never did make a collaborative blog for those interested in systems biology, but it was not for lack of interest.

I’m going to make a point of trying to post more sciencey topics here in the future.

The XKCD comic “Dream Girl” references a time this weekend, at a park in North Cambridge, MA. I can’t make it, but I’d love to hear what happens from anyone who does go! The XKCD forums suggest that the original comic was actually altered to prompt this meeting.

(I learned of this from a Facebook group inviting people to show up at the park).

I find it puzzling when I give a scientific presentation and when I reference some author, someone in the audience asks a question prefaced by “I know that author very well.”

Should I be thinking: “Oh! You know them? I guess I’ll actually pay attention to you now!”

Or maybe: “Normally I would have assumed that you were unqualified to ask me a question, but obviously I misjudged you. If you slip me a copy of your resume after the talk I’ll check whether you are fit to eat lunch with me.”

I’m being facetious here. It’s probably just their way of showing that they really care about the question that they are about to ask.

Right?

The ADA recomends that we clean between our teeth with floss every day.  I’ve never kept up with that schedule - I haven’t even come close - and I don’t think anyone else real or fictional does it either.  I think at maximum I floss once per week, and on average it’s probably once every few weeks (back when I had braces I flossed less than once per month). 

At the same time, in my life I have only had two cavities, and I attribute those to my moving to a city that does not add fluoride to the water supply.  Besides that little hiccup, my dentist always tells me that I do a great job cleaning my teeth and to keep up what I’ve been doing.  I do brush 2-3 times a day.

I like my teeth, and I don’t want to have them replaced.  They don’t grow back, it stinks.

So before I moved to New Mexico, I implemented one of my short excercises in self-discipline.  I committed to flossing once every day for seven days. 

The first day I had the normal pain from not flossing for a few days.  The second day wasn’t so bad either.  By the third and fourth days, I really wanted to stop.  The flossing didn’t look like it was doing anything catostrophic — there was no blood — but it hurt quite a bit.  And the pain didn’t stop after I flossed.  It lasted all day…  It wasn’t excruciating, rather it was annoying.

I made it through the seven days, and I was glad to be done with it when I stopped.  I decided to go back to my weekly flossing routine.

The one benefit I did notice was that now when I do floss  it doesn’t hurt at all.  I think I worked out some of the “kinks” in my gumline.

I’ve been mostly blog-silent for a while now.  The main reason is that at the end of May I moved to New Mexico to take a temporary research position at a government lab.  New Mexico has been surprisingly entertaining.  It’s a beautiful place.

The whole state is also pretty high up (~5000-7000 feet), and this makes for a great, low-humidity summer.  I used to think I hated warm weather, but it turns out I just can’t stand humidity!

Now that I’m settled in here I am hoping to pick up blogging again.

Yesterday O’Foghlú sent me a link to Flickrvision, a site that combines the Google Maps and Flickr APIs to produce a real-time sampling of photos being uploaded to Flickr.  It’s strangely a addictive and dynamic snapshot of what people are doing around the world.

For a long time now I’ve felt been stuck in a rut.  I have goals, but I find myself making little or no progress towards those goals.  Worse yet, I seem to be losing my ability to accomplish goals that I used to take for granted.

An easy example is running.  Many years ago, I ran every day, without fail.  A lot has changed since then, so I don’t expect to be able to run quite so much now.  I’m usually able to attribute my running, or lack-thereof, to external factors.  “I’m not running now because I’m a fair-weather runner,” or, “I am running now because I have to get in shape for a race.”  In either case I do it because of circumstance, rather than as part of a plan.

A more recent example is that I have extreme difficulty reading scientific literature at my job.  In general, I can read 1 paragraph before I literally lose consciousness and take a 2-hour nap (don’t tell my boss!).  The advent of coffee in my life does some to ameliorate this, but again my performance is not consistent.

Running and reading are two things I’d like to be good at.  They are both things that I start many of my days intending to accomplish, but more often than not I do neither.  This lackluster consistency is ubiquitous in my life now… in work, in exercise, and even (perhaps paradoxically) in leisure activities.

I don’t think I’m inherently bad at work, excercise, or leisure.  It’s more a lack of discipline.  I realize now that I have not had well-developed self-discipline anytime in my adult life.

And that’s OK.  Discipline isn’t something we’re born with.  We have to learn it.  Everyone learns differently, and I know from personal experience that I learn best by example, experiment, and practice. 

So, over the upcoming indeterminate period of time, I’m going to practice self-discipline in small, well-planned, exercises, until I get it right. 

I’ve been a big fan of the Gmaps Pedometer site since they first took advantage of the Google Maps interface.  I just heard about a newer route mapping site called Running Map.  This Yahoo-Maps based service has a number of features I’ve been waiting for in Gmaps.  You can plot routes using single clicks, chart the elevation changes of a route, there seems to be better satelite resolution for the area where I live, and it just has a cleaner interface.

These sites aren’t just for runners…  I use them to map out my walking routes to work and find out which ones really are the shortest.  Check them out to help get an idea of how much moving you do each day.