Category Archives: Alchemy

Self Empathy

I have never been into meditation, but today I tried an experiment.

When I got into my car on the way to work, I sat for two full minutes with my eyes closed an the engine off. During these two minutes, I repeatedly gave voice to the feelings and sensations I was aware of. Each time I felt something I said “I am aware that I …”, where the blank was the sensation I was experiencing. I said things like:

“I am aware that I am hearing a plane fly overhead.”
“I am aware that I am stressed about a project I have to work on today.”
“I am aware of the feeling that I have to go to the bathroom.”
“I am aware that I enjoyed time with my friends this weekend.”
“I am aware that despite having a good weekend, I am judging myself for not accomplishing enough.”
“I am aware of the feeling of the sun shining through my car window.”

The goal was not to place judgments on any of these feelings or inner interpretations, but rather just to acknowledge them. I found myself wanting to follow “I am aware that I feel …” with “and that means I should…”. I tried hard to veer away from those thoughts.

At the end of two minutes I felt relaxed, but the real impact was more subtle, and over the course of the day. I acutually found myself more conscious of what I was thinking and feeling, and a bit less reactive in interpersonal situations. It wasn’t perfect, and quite often that awareness came only in retrospect, but it was somehow refreshing to hear the words “I am aware that I” going through my head spontaneously.


Posted by on May 31, 2011 in Alchemy


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Using LaTeX with Microsoft Word

In grad school I wrote as much as I could in LaTeX, including my Ph.D. thesis. This offered several advantages, the largest being that it enabled me to script the generation of very large tables (50+ pages) automatically. If I made a change to my project that affected the output of said tables, all I had to do was rerun the script that generated those tables and my thesis would be updated.

The biggest drawback was that occasionally I have to submit manuscripts to publishers who either will not accept LaTeX submissions, or who seem to go out of their way to make submitting in LaTeX extremely difficult.  Similarly, sharing documents with collaborators in LaTeX can be frustrating.  Sure, you can send the PDF, or maybe they are even comfortable editing the LaTeX directly (rare in my experience), but I have yet to see an end-to-end procedure for tracking changes made by peers in a PDF or LaTeX document that makes it easy for me to accept or reject the changes.

There are a few tools available that can help make converting your LaTeX projects into Word format a few steps better than retyping your whole thesis (though it’s still pretty painful!):

  1. LaTeX2rtf will help you convert your LaTeX document to a Rich Text Format (RTF) file that can be opened in Word.  This will leave you with a lot of formatting fixes to implement, particularly for any tables, figures, equations, etc., but I find it’s better than having to start from scratch.
  2. Bibtex4Word can format your entire bibliography in Word using Bibtex bibliography files as the reference source.  This means you can use all those old .bib files you’ve created for LaTeX in word documents!  I find the particularly useful if I know I need to use Word for a project but I don’t want to have access to RefMan or EndNote.  I also recommend JabRef for managing BibTex files.

Recently I’ve been struggling to format a paper for Nature Molecular Systems Biology.  They accept LaTeX submissions, but for ease of sharing my manuscript with my collaborators I decided to write it in Word.  Unfortunately Nature does not provide a BibTex style file for Nature MSB, so in order to use Bibtex4Word I was forced to make my own using makebst.tex.  Luckily, the Endoplasmic Reticulum blog documented their struggle with making a BST file for Nature MSB and I was able to make a BST file without too much trouble.  Note, however, that to use this BST with Bibtex4Word you’ll need to make use of some style flags.

I should clarify that this is all a terribly convoluted process and there are definetely bugs you’ll encounter along the way.  If you want the simplest end to end solution, invest your time and resources in a solution that’s specific to Word, or specific to LaTeX.


Posted by on March 20, 2011 in Alchemy


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Values in Science – How to Judge Scientific Posters

(apologies if this post isn’t super clear — I just wanted to get it out)

I haven’t posted in ages, but I am at a conference, I can’t sleep, and something is on my mind, so I figured I’d strike while the iron is hot.

I’m at the 2010 Computational Science Graduate Fellowship Fellows Conference in Washington D.C. This evening I had the pleasure of serving as a judge for a poster competition. The current fellows present posters on their graduate research. The poster topics shared the theme of “computational science”, but besides that they can be from any discipline. I’m not going to discuss the specifics of the posters here.

The basic criteria we judged posters on were visual, oral, and impact.

To me, there are fundamental rules governing effective poster design. For example, in the visual category, use no paragraphs of text, and large fonts (even in figures), and well balanced graphics. In the oral category, have a 3 minute speech prepared, and refer to the poster when delivering that speech. I was surprised, however, how other judges had vastly different values when evaluating the work submitted. Most specifically, some judges felt that work of high scientific quality could compensate for poor poster presentation.

Have you ever designed or seen a scientific poster? If so, what do you think are the most important criteria for evaluating this sort of work?


Posted by on June 24, 2010 in Alchemy


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The Big Finish

Apparently the Diesel Wi-Fi terms-of-service requires users to blog.

So here I am.

In the next six months, my three major activities are:

  1. TA a “drug delivery” class (provides current income).
  2. Finish and defend my thesis.
  3. Find a job (provides future income and intellectual fulfillment).

TAing isn’t so hard to fit in because it’s scheduled into the academic year.  I go to class twice a week.  Immediately after class, I review the notes for the class using a codified note-taking system.  Once a week, I hold office hours.  Three times this semester, I’ll have to grade about 90 exams.  These activities fit themselves into my schedule.

It can be harder to make time for dissertation work and job searching.  Essentially, these are both full-time jobs being fit into a single set of full-time man-hours.  Overscheduling seems to be the hot business strategy in this economic downturn, however, so I’m trying to view this over-commitment as my way of cutting back (“I had to let the guy who normally applies for my jobs go — we just couldn’t justify his salary to corporate in this climate.”)

I’ll let you know how it goes.

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Posted by on September 8, 2009 in Alchemy, Garbage In, Garbage Out


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A Million Little Files

My office desktop’s Windows partition fills up on a weekly basis (I usually notice first when CNN news videos start to quit unexpectedly), so I’m always looking for some way to search for and destroy large files or folders on Windows XP and free up disk space. Usually this involves clever guesses and manual breadth-first searches on my computer.

Enter WinDirStat. This program combs the hard drive for you and helps get detailed information about where larger files are hiding. This is not a review of the program, nor it is an endorsement, but I’m a fan of pretty pictures, so when I saw this I couldn’t help but say something.

WinDirStat output

The graphical output at the bottom visualizes all the files on your drive, as well as their relative size. With a few clicks, I cleared ~3 GB of space.  The main culprits were the “sharing folders” in MSN Messenger (a program I no longer use) and various cached installer files.

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Posted by on August 24, 2009 in Alchemy


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Newton Fractal Visualization with Python

I felt like trying something new, so I wrote a Python script to plot Newton’s fractal.

Newton's Fractal (30 iterations, 1500 x 1500 resolution, 1e-6 convergence)

This graphic shows the time to convergence for solving z^4+1 = 0 using Newton’s Method.  The solution to this equation is one of four possibilities, which are represented using the colors red, blue, green, and yellow.  The solution that Newton’s Method returns depends on the initial guess.  I plotted the final solution for initial guesses in the range 0-1 (real, horizontal axis) and 0j-0j (imaginary, vertical axis).  Color depth represents faster convergence to a particular soltion (i.e., brighter pixels represent initial guesses that converge to a solution faster).

The script is based heavily on Listing 7-1 from “Beginning Python Visualization” by Shai Vaingast. It’s a good book with other fun examples, but my code for this problem is here.

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Posted by on August 13, 2009 in Alchemy


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Pearl Harborer

Last year at Zandperl’s Halloween party we were playing “The Coachride to the Devil’s Castle” (aka Die Kutschfahrt zur Teufelsburg), and we spontaneously came up with the following definition of “Pearl Harborer”:

Pearl Harborer

In the Card Game “Die Kutschfahrt zur Teufelsburg” (“The Coachride to the Devil’s Castle”), a Pearl Harborer is someone who is surreptitiously hiding the “Schwarze Perle” (a.k.a. “Black Pearl”) card.

Brian’s going to declare victory this turn, unless he’s a pearl harborer…

I submitted this definition to Urban Dictionary.

It was rejected.  Superficially, that’s not a big surprise, nor do I care.


What surprised me, initially, was that it took so long for them to get back to me.  I submitted the entry on October 27, 2008, and received my “entry not published” email three days ago.

Peer review is known to take ages, but still I could not imagine why the rejection would be so slow (compared to Wikipedia rejections, which can happen within minutes).  But the real surprise here is that Urban Dictionary has standards at all. The rejection letter came with a link to Urban Dictionary’s publishing guidelines (you may need to sign up to see the link):

As an editor, you decide what gets published. Use these guidelines while you make your decisions.

1. Publish celebrity names but reject friends’ names.
2. Publish racial and sexual slurs but reject racist and sexist entries. 
3. Publish opinions.
4. Publish place names.
5. Publish non-slang words. Ignore misspellings and swearing.
6. Publish jokes.
7. Reject sexual violence.
8. Reject nonsense. Be consistent on duplicates.
9. Reject ads for web sites.
10. Publish if it looks plausible.

So anybody can sign up to be an editor, and some consensus of arbitary/random editors decides which entries get accepted and which get rejected.  According to these guidelines, my entry should have been published.  However, whichever editors saw it disagreed, probably because they didn’t “get” the definition, so now it’s lost to the world forever.

The sad part is that this isn’t so far off from academic peer review.  Sometimes you discover or create knowledge that you know is right, and you try to put it out there but the people reading it don’t think it should be seen, and they reject it, often with little or no explanation why.  If it’s this hard to publish in the haphazard, anything goes environment of Urban Dictionary, imagine how hard it must be to publish in a journal, where entries theoretically have consequences.


Posted by on January 27, 2009 in Alchemy, Entertainment


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1280 x 960

In 2008, I resolved to run 1000 miles.  This was a good resolution because it was quantitative, yet long-term, and challenging, yet achievable.  This year I want to resolve to do something that also meets these criteria, but I don’t want to just repeat my 2008 resolution.

I liked the running resolution in particular because I got something tangible out of it.  I’m in the best running shape of my adult life.  I feel good when I run.  I’ve improved my health and fitness.  Now I want to do something similar for my brain.

Recently, I realized that I’ve been learning more at the local trivia night than I have been working on my Ph.D. research topic.  This troubles me.  School is for learning, right?  So what am I doing wrong?  Part of the problem is that graduate research can have little tangible gratification along the way.  There are no grades.  We never feel the sweet release of final exams.  There isn’t always a clear measure of progress.

With that in mind, I wanted to make 2009 a year for learning new skills.  I made a list of goals for things to learn/practice over the course of the year.  It had everything from picking up a new instrument to doing 100 consecutive push-ups. This was a fun list to make, so I’m going to save it in a draft on my blog even though I eventually decided not to make it a part of my 2009 resolution.

Instead, I decided to take the practical route:

In 2009, I will finish my Ph.D. project, write my dissertation, and defend my thesis.

From my current vantage, this seems about as likely as a herd of cats carrying me to school tomorrow on their backs.  From your perspective, on the other hand, it may seem like a cop out to resolve to do something that I am pretty-much on track to do anyways.

But I assure you, this is not going to be easy.  I’ve been working on…  stuff…  for five years now, and I feel I have very little to show for it. Making this thesis happen is going to require discipline, planning, and maybe if I’m lucky, some learning. My running resolution was a success largely because of the logging and reporting I did throughout the course of the year. Completing my thesis will require a similar attention to progress.  I could record pages over time, or just blog more frequently about research, but I’m open to hearing any suggestions for reaching this goal.

What are your resolutions for 2009?


Posted by on January 7, 2009 in Alchemy


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I Would Run 1000 Miles

Early in 2008, I made a New Year’s Resolution to run 1000 miles over the course of the year.  I liked this resolution from the start – it was quantitative, attainable, challenging, and spanned the entire year.  There were ups and downs, but with a few days to spare in December I hit 1000 miles (total mileage: 1013 miles).  I’m left with a really happy trend in my mileage over the last 8 years:


I’m ecstatic I’ve been able to incorporate running into my life more substatially every year since I started grad school.  I’m not expecting another 30% increase in mileage for 2009, but I do think I can make good things happen by continuing consistent running.

An unexpected feature of the seasonal mileage pattern for the year was that I actually ran more in the winter-spring season than in the summer or fall:


In this chart, “WS” is the Winter-Spring season (January-April), “S” is the Summer season (May-August), and “F” is the Fall season (September-December).   Compare the winter of 2008 to any other winter and the difference is striking.  My mileage drop off in the warmer months is due to a number of factors — injury, illness, meeting my current girlfriend, but I’m really glad I put those hard miles in early.  Those up front miles made the 1000 mile goal possible.

I’ll close now with a collection of all my running posts from the year, but I promise another post with my 2009 resolution soon.

Running posts from 2008:


Posted by on January 6, 2009 in Alchemy, No Easy Days


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Evil, Robot

This research project to develop a computer simulation of a truly evil person definitely seems to be pushing the limits of the three laws of robotics.  To extend this work, I’d like to see a new version of the Turing Test (the Evil Turing Test?) to see if a human judge can reliably tell the difference between the following pairs of test subjects:

  1. an evil computer from a good computer
  2. an evil computer and an evil human
  3. an evil computer and a good human

… although a machine that can pass tests 2 or 3 is technically passing a special case of the Turing Test too.

Story via Science Made Cool, post inspiration via O’Foghlú.

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Posted by on October 28, 2008 in Alchemy


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The Genetic Carry-On Limit

Flying through Philadelphia is practically the same as asking to lose your luggage. As I wait at the baggage claim for a suitcase I know won’t come, I wish I had listened to my mother and squeezed everything into a carry-on.

Packing for a flight reminds me of a game I played in elementary school, in which we had to list five items we would want if we were stranded on a desert island. I always listed television, my best friend and ice cream, but, for some reason, never a boat.

It’s the same question we face every time we travel. What should we bring, and what should we leave behind? Deciding what to pack is almost equivalent to the philosophical question of what you need to survive and be comfortable.

I think about problems like this a lot…

I wrote an essay (here, page 5) attempting to convey the philosophy behind my research project, and it landed an honorable mention in a writing contest. This led to the nice result of getting to work with a professional copy-editor before the essay went to print, and they gave me a lot of insight into how to tighten up my writing for a general audience. A nicer result was feeling like I had a little win with regard to my research, and those wins seem to come few and far between recently.

Thanks to Jason and Gretchen for help editing my original essay.

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Posted by on October 8, 2008 in Alchemy


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Activism Energy

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.

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Posted by on July 8, 2008 in Alchemy


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Abortion Used as Art

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.


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.


Posted by on April 17, 2008 in Alchemy


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Bill Nye Photos

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.


Posted by on April 4, 2008 in Alchemy, Photos


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The Science Guy

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.


Posted by on March 28, 2008 in Alchemy


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