Transylvanian-American Awareness Day

Just in time for Halloween, Sesame Street’s “The Count” is here to remind us that not all famous leaders in modern-day Romania are bloodsuckers.

Not all romanian aristocrats are bloodsuckers!

Intelligent Drug Design

It’s one thing to insist that creationism be taught in schools, but what would the world be like if we really took intelligent design seriously? Probably something like this…

Pfizer to launch new “Intelligent Drug Design” working group

NEW YORK- Pharmaceutical giant Pfizer today announced a three year, $32 million drug discovery initiative targeted mainly at diseases prevalent in developing countries. However, although seemingly a small effort by the standards of the drug industry- Pfizer alone spent $9.4 billion on overall research and development in 2010- the program has already stirred considerable debate.

According to Pfizer spokeswoman Susan Nym, the new program will be based not on evolutionary biology- the traditional cornerstone of pharmaceutical research- but rather on the hypothesis of Intelligent Design, which contends that life was created by a supreme being. This new drug discovery initiative was quickly praised by supporters of intelligent design, who have long been dogged by criticism that the theory lacks testable predictions or research applications.

The decision to participate in the new “Intelligent Drug Design” initiative was an easy one, Nym says. With the looming expiration of patents on several highly profitable drugs, Pfizer needs to find new hit drugs- and soon- to offset lost revenues. However, traditional evolution-based methodologies usually take many years of investigation and clinical trials before a new drug can be cleared for sale by the FDA.

“What Pfizer needs”, says CEO Ian Read, “is a miracle. And who better to give us one than our supreme creator?” Analysts have reacted favorably to the news, pointing out that the choice to target third-world diseases should increase the odds of success, while growing political support of ID-based research could well cut years off the time-to-market. The new unit, which Pfizer has recruited leading ID researcher William Dembski to lead, has been described as a low-cost way to explore an emerging field; should it prove successful, other diseases, such as arthritis, may follow.

Of course, even proponents of intelligent design admit that traditional evolution-based research will never go away completely. “My first task on the job was to cancel the erectile dysfunction project”, noted Dembski. “But this initiative clearly shows that intelligent design is a viable scientific theory, and I look forward to¬† performing cutting-edge research alongside the visionaries at Pfizer.”

Pfizer stock rose 5.8% on the news.

The other sides of teaching

Teaching involves many things that fall outside the classroom. To celebrate the academic new year, here are two reminders that there’s always room to improve, even on the most mundane tasks.

Turnitin, the plagiarism detection service, has apparently been offering students a paid service that helps to evade its own filters. In the process of investigating whether it’s specific enough to be dangerous (hint: yes), the author of that article also makes the interesting point that Turnitin’s database is itself quite limited, in particular with regard to copyrighted works such as newspaper articles. (Newspapers and professional writers can, after all, afford to mount a major legal offensive… unlike students) The database of matchable content is central to the effectiveness of their service, so it’s understandable that the company is a bit cagey about exactly what books and periodicals aren’t in their collection of “90,000″ such items. (I will point out that 90,000 items is nowhere near comprehensive: for comparison, the University of Michigan’s library contains some 10 million items, and in 2008 was estimated to be growing at 177,000 items per year. If we limit ourselves to digital books offered readily for sale, there are 950,000 items in the amazon kindle store at present)

If you have a very specific source (or group of sources) that you want to compare a paper to, and if you have those sources in digital form on your computer, then open source tools like wcopyfind might be a viable alternative (or complement to) database-based for-pay services like turnitin. No automated tool will relieve instructors of the need to talk to their students about plagiarism and have a solid policy in place… but while I’m not crazy about automated plagiarism detection services, the sad truth is that some form of due diligence is always going to be necessary when grading.

On the lighter side, this post on syllabus design may be of interest. Although the final result goes a bit overboard with graphical effects, there’s little doubt that the standard layout of course syllabi is far from ideal, and finding key information is often a game of hide-and-seek. What I like about the final layout shown is that key information is easy to find: what doesn’t fit on the front page is highlighted and set apart from long paragraphs, and/or clearly pointed to with a table of contents. There’s plenty of literature on usability in print and web design that would apply equally well to printed/PDF handouts, and for a document as frequently referenced as the syllabus, the extra investment of time and energy might be worthwhile.

When you think white coats and padded walls, think science

After mentioning to a bank teller that I do scientific research, I was greeted by the familiar reply:
“Oh, so you’re one of those really smart people who wears a lab coat and goggles?”

At present, my work is largely done at a computer, so I’m never sure quite what to make of such comments. For those occasions when time constraints don’t allow me to respond constructively, my first thought was to make one of these. (if you’re going to be trapped in the stereotype of lab coats, then at least have fun doing it)

…But the truth is that all those LEDs would make it very uncomfortable to wear while sitting down. For those of us whose work takes us away from the bench, I propose following the lead of one theorist I recently met: tie dye lab coats!!! The ones linked appear to be of the style favored by chemists (buttons and loose sleeves) rather than biologists (snaps and elastic cuffs), but the basic idea is the same.

Quick and dirty image randomizer

While doing a little maintenance on this site, I decided to have fun with the 404 pages by adding random images. In the process of tracking down a crude implementation, I found several sites that wanted $10 or more for what is- as it turns out- a very short snippet of code. That price struck me as rather excessive.

So without further ado, here’s my crude implementation.

#!/usr/bin/env python
# The above line is mandatory. The other comment lines can be safely removed.
import random, os
# Get a list of files in a specific directory, and choose one at random
files= [ f for f in os.listdir('../images/randomizer') if os.path.isfile('../images/randomizer/' + f) == True ]
chosenfile = random.choice( files )
# Print the final name of the chosen image
# Strip the path provided by the script first and replace it with a relative path that makes sense for the HTML page
# (this requirement is a side effect of my directory organization: script and image directories are
# both subdirectories of the main site)
print "Content-type: text/html\n"
print "images/randomizer/%s" %os.path.split(chosenfile)[1]

The script- a mere six lines of code without comments- outputs a string of text with the filename of the chosen image. I wasn’t able to call it directly from an image tag, so instead I used a server side include (some servers require using the “.shtml” file extension to run SSIs). Thus, the script is incorporated into an (s)HTML page to produce a random image as follows:

<img src=<!--#include file="scripts/"-->>

You can see the script described above in action at my 404 page. If you just want to load the script directly and display a random image (and nothing else), then you’ll have to change the line of code that prints the header information, depending on the image format chosen. There are good instructions here.

Quick, simple tech support requests

One downside to doing research with a computational aspect- or indeed, any work that entails proximity to computers- is that you become pigeonholed as “the tech support person”, asked to help with finicky software, spills, or, such highly technical questions as how to turn on a cell phone. (In the latter case, I was being called from the phone in question. True story.)

While it’s tempting to just send your loved ones to the the XKCD flowchart or snarky search reminders, not every technology problem can be solved so easily. If you often find yourself mired in solving difficult issues based on vague information, then you know the importance of a well structured Q&A. Now available for public use, I’ve created a web form that asks for a variety of helpful information and emails the results to any specified recipient.

Feel free to try it for yourself:

This was done as a very quick project to teach myself CGI scripting, and there are still some rough spots (such as kludgy instructions). Suggestions or bug reports are welcome, and the source code may be made available in the future if there is interest.

Lastly, a note on privacy: the information and email addresses provided will not be saved, but I am logging user IP addresses to monitor for abuse. Please refrain from using this (or any web service) to send “enlarge ur hard drive” spam.

Gratuitous acts of empiricism

I came home to find a message on my machine, asking me to call back and confirm the details of my windshield replacement.

My initial reaction was to delete the message, assuming it was a wrong number- after all, my car was fine the last time I checked. But as my finger hovered over the button, I thought to myself:
“Wait! I’m a scientist!”

So I walked over to the window and looked at my car. Then, I deleted the message with confidence.

Someone is missing out on a really effective business model. And that’s a good thing.