The Big Finish September 8, 2009
Posted by halfawake in Alchemy, Garbage In, Garbage Out.Tags: activities, dissertation, grad school, jobs, science, TA, teaching, thesis
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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:
- TA a “drug delivery” class (provides current income).
- Finish and defend my thesis.
- 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.
A Million Little Files August 24, 2009
Posted by halfawake in Alchemy.Tags: clear hard disk space, disk full, GB, hard disk, hard drive, hark disk space, MB, space, WinDirStat, windows, windows xp, XP
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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.
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.
Newton Fractal Visualization with Python August 13, 2009
Posted by halfawake in Alchemy.Tags: fractals, newton's method, python, visualization
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I felt like trying something new, so I wrote a Python script to plot Newton’s fractal.
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.
Pearl Harborer January 27, 2009
Posted by halfawake in Alchemy, Entertainment.Tags: card games, coach ride to the devil's castle, Die Kutschfahrt zur Teufelsburg, halloween, pearl harborer, peer review, urban dictionary
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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.
1280 x 960 January 7, 2009
Posted by halfawake in Alchemy.Tags: 2008 Resolution, 2009 Resolutions, goals, grad school, learning, research, resolutions, running, science, thesis
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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?
I Would Run 1000 Miles January 6, 2009
Posted by halfawake in Alchemy, No Easy Days.Tags: 2008 Resolutions, goals, resolutions, running
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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:
Evil, Robot October 28, 2008
Posted by halfawake in Alchemy.Tags: ai, evil, laws of robotics
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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:
- an evil computer from a good computer
- an evil computer and an evil human
- 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.
The Genetic Carry-On Limit October 8, 2008
Posted by halfawake in Alchemy.Tags: compose, CSGF, DOE, essay, krell, krell essay contest, minimal cell model, minimal gene set, packing problem
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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.
Activism Energy July 8, 2008
Posted by halfawake in Alchemy.Tags: congress, energy, energy policy, frank, hinchey, kerry
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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.
Abortion Used as Art April 17, 2008
Posted by halfawake in Alchemy.Tags: abortion, creative fiction, hoax, performance art, pro-choice, pro-life, Shvarts, yale
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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, 2008Ms. 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.
Bill Nye Photos April 4, 2008
Posted by halfawake in Alchemy, Photos.Tags: bill nye, bob dole, communication, media, message, PCST, science
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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.
The Science Guy March 28, 2008
Posted by halfawake in Alchemy.Tags: bill nye, PCST, science, science communication
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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.
Blogging as a Way to Think February 22, 2008
Posted by halfawake in Alchemy.Tags: Blogging, blogs, clive thompson, communication, PCST, science
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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.
Filing System for Research Papers February 21, 2008
Posted by halfawake in Alchemy.Tags: filing, grad school, inbox zero, organization, papers, research
7 comments
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.
Ancient Blogging Wisdom February 20, 2008
Posted by halfawake in Alchemy.Tags: Blogging, blogs, communication, design, PCST, science
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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:
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“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.
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“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).
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“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.
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“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.
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“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!”.
