Monthly Archives: December 2006

Give the Gift of No-Obligation

Each year I make a list of who I want to give Christmas gifts to, check it twice, and spend several weeks sorting out who should get what.  I try to make the gifts meaningful, because I usually only give gifts to those who have played had some important role in my life that year.  I also usually don’t get gifts for people who I won’t see during the holiday season, with a few exceptions.

I really don’t care if I receive any gifts.  I mean I really actually do not care at all.  This is not to say that I don’t appreciate the thought behind gifts, but more often than not the gifts that I receive just clutter up my life (“oh – a photo album!  Wow…  that will go perfect next to the other six I got from you.  Yeah..  Wow thanks.  Yeah…”). 

In general, if I get a gift for someone, they will feel pressure to get me something in return.  Furthermore, sometimes getting a gift for someone one year sets up a pattern that must be repeated in the future; I don’t like making someone feel they have to get me a gift just to keep the score even.

Some friends give clear messages about receiving gifts.  For example, I got Sasha a bithday gift this year, and her response on receiving it was, in short, “what is wrong with you people and your gifts!”  Despite the unexpected harshness of this message, I took it to be a no-nonsense indication that Sasha doesn’t want gifts from me anymore, and that’s fine.  I’d much rather get a message like this than make Sasha feel like she needs to start buying me gifts.

Maybe thinking about it this much betrays the point of the holiday season.

The important part of this season is not the receipt of gifts, nor is it giving them.  The season, to me, is about the spirit in which we give gifts.  It’s an ackowledgement of those around us and the roles they play in our lives.  That can be accomplished easily without wrapping paper, scissors, or tape.

Merry Christmas everyone.

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Posted by on December 25, 2006 in Garbage In, Garbage Out


The Climb

I’m somewhat of a fair-weather runner…  And when I don’t run, I tend not to do any exercise, so come Spring time I’m usually usually a wad of cookie-dough waiting to be transmuted into some sort of (soft) carved wood.

This winter was not supposed to be any different.  I took the last four weeks off.  The arrival of sub-freezing temperatures is usually accompanied by a busier time of year for me, so the cards are stacked against exercise and it’s usually the first thing to go come December.

But the Northeast has experienced a strangely warm winter thus-far, and “busy-time” just ended.  Now I’m on vacation from work for the holidays, I have nothing to do, and it’s relatively warm out.  So today, I went for a run.  It was just 1.5 miles proceeded by some light calisthenics, but that was sufficient to wear me out.  Half a mile into the run I was breathing hard, my muscles were all prickly from the unfamiliar increase in blood flow, and my motivation was back in bed dreaming of not-running.

I always wonder why I feel like I get out of shape so fast.  It takes months for the thought of a 4 mile run to stop making me cringe, but I can regain that trepidation in a matter of weeks.

In any case, if this warm weather persists I’m hoping to get a healthy jump on the Spring season.  In case it does get cold again, I’d be happy to hear anybody’s suggestions for how to stay fit in the cold months.

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Posted by on December 23, 2006 in No Easy Days


If Your Eyes Are Exposed to Pacman…

If Your Eyes Are Exposed to Pacman…

… then proceed to the nearest suitable source of water for irrigation.

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Posted by on December 13, 2006 in Photos


Life of Pie

A couple friends from home once suggested an analogy for life based on a pie (A.E. and R.P.).  This is my interpretation of their analogy.

Life of PieThe basic idea is that you are a pie…  A delicious pie with slices of a variety of sizes and flavors.

Each piece of your pie represents a part of your life that you need fulfilled by a person.  Slices could represent any parts of you, emotional, physical, or spiritual.

Not everyone likes every flavor of pie.  For example, let’s say your slice of pumpkin pie represents your desire to shoot skeet with your friends.  Not everyone likes pumpkin pie (which, in this example, is analogous to clay pigeons), so not everyone will be able to fill that slot.  Some of your friends, as much as they like you, won’t be able to satisfy that slice of you, because that slice doesn’t sit so well with them.  You can’t usually commission every facet of your life to a single person, so you associate with a group of people who get to come enjoy your dessert.

When people look at you, they don’t always take the time to look at all of your slices.  Some only see a small piece.  Maybe that small piece so ardently attracts their attention that they never get to see the rest.  This fixation may prevent them from getting to know the real you, but that also might be a piece that no one has ever tasted before, even those who have sampled most of your pie.

There are some slices that nobody eats but you.  Those are the parts of your life that you prefer to enjoy alone.

To confound the issue, your pie is changing.  As we grow we assign new weights to the parts of our lives, and the pie pieces grow larger or smaller accordingly.  New slices appear, and some vanish altogether. 

I think the pursuit if happiness is the continual  restructuring of our lives in such a way as to get as much of the pie eaten as possible.

Thanks to A.E. and R.P. for the inspiration.


Posted by on December 10, 2006 in Garbage In, Garbage Out


An Inquiry Driven Blog

On December 6th, the folks at the WordPress blog annoucned a call for ideas on how to use 10GB of space in a blog. This post is one such idea.

Note: it occured to me that perhaps the original post for this topic was blocked from pinging back correctly since it had several links, so I’m posting it a final time. If you’re interested in seeing the links that I originally posted, see the previous post.

Blogging is an important link between professionals across a wide range of fields and the public. It’s a great way for enthusiasts of a field to communicate with a wide audience. This presents an opportunity for developing a resource for inquiry-based learning. The goal of inquiry in the classroom is to promote students to ask about the world and how it changes rather than to just memorize facts. Inquiry learning is most easily accomplished in the classroom when the instructor has access to project-based course material that has been developed ahead of time.

With 10GB of space available, I would develop a blog for collaborative production and discussion of inquiry-based projects for learning about computational biology. This topic would lend itself to blogging more than traditional biology because the medium for blogging is the same as the medium for computational inquiry (i.e. a computer).

Biotech and Nanotech

image credit: U.S. Department of Energy Genomics:GTL Program,

Blog Features

The blog would have several contributing authors who could design projects for a variety of topics and keep content updated regularly.

– The content of a project would include instuctions, videos, pictures, and downloadable programs.

– Contributors would upload their projects in a variety of formats geared towards different levels of education (K-8, High School, College).

– For undergraduate level applications, models would be available in SBML, CellML, MATLAB, and other commonly used modelling formats.

– Site visitors could ask questions or review models that are available using the commenting features of the blog.

– Current events in science could be posted to the blog and linked to the project posts/pages, so that teachers could always draw on modern motivation for the lessons.

– The projects would include videos of simulation results and experimental systems that correspond to the simulations.

Why isn’t this already available?

While there are several repositories of biological models, available online, none has the collaborative feel of a blog. This makes them less ammenable to education below the graduate level. A weblog interface represents a good middle ground between a database and a forum.

Why does this require alot of space?

Depending on how WordPress changes its upload policy this blog could include large images, pdf documentation, videos of simulation and/or experimental results, and computational modelling tools.

I’m open to suggestions on how to improve this idea. Thank you!


Posted by on December 9, 2006 in Alchemy


Tags: ,

An Inquiry Driven Blog – Links

These are the links relevant to the Inquiry Based Learning post above.

– inquiry-based learning

10GB of space available

computational biology


– repositories of biological models

-potential changes to the Wordpress upload policy

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Posted by on December 8, 2006 in Alchemy


It’s Not Paranoia if I Really Am Out to Get You

I just took a personality disorder test I found linked from The WHY Chromosome blog.  My results, compared to the average of those who took the quiz, are:

Halfawake’s Personality Disorder Test Results

Disorder Score Avg.
Paranoid |||||||||||||||||||| 82% 49%
Schizoid |||||||||||||| 58% 53%
Schizotypal |||||||||||||||| 62% 53%
Antisocial |||| 14% 47%
Borderline |||||||||| 38% 47%
Histrionic |||||||||||| 46% 43%
Narcissistic |||||||||| 38% 41%
Avoidant |||||||||||| 46% 38%
Dependent |||||||||||||||| 62% 37%
Obsessive-Compulsive |||||||||||| 42% 40%

I fall within ten points of average for all the categories except Paranoid, Antisocial, and Dependent.  In this quiz, those maladies are defined as:

Paranoid Disorder – individual generally tends to interpret the actions of others as threatening.

Antisocial Disorder – individual shows a pervasive disregard for, and violation of, the rights of others.

Dependent Disorder – individual shows an extreme need to be taken care of that leads to fears of separation, and passive and clinging behavior.

So I already know I’m rather Paranoid.  I call it a defense mechanism.  It’s no surprise that I score high on the Dependent scale either; I still have nightmares about the Jolly Green Giant coming to take away my loved ones.  After reading the definition of Antisocial I’d say that I’m proud to have a low rating there, but maybe that score only results from my fear that by violating the rights of others I’ll provoke their threats and/or loose their support.

I have fond memories of taking the Kingdomality Personality Test many years ago…  I came back with the result “Black Knight“, and nobody else I knew got that result, not even my evil friend Earl.  I was proud of my Black Knight title, and chose to abstain from ever taking the Kingdomality Personality Test again, lest I be labeled something less intimidating like a Jester or a Benevolent Moblin. 

These tests are fun sometimes.  If our purpose in life is to follow a path of discovery leading to who we are, there’s nothing wrong with reading a few computer-generated signs along the way.


Posted by on December 7, 2006 in Garbage In, Garbage Out


Future Corporate Tools

Future Corporate Tools 

Photo opportunity noticed by O’Foghlú.

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Posted by on December 5, 2006 in Photos


My Whole Life is a Lie

For over fourteen years (until about an hour ago), I’ve believed in the apparent lie that the famed Coriolis Effect was responsible for toilets and sinks draining one way in the Northern Hemisphere and the opposite in the Southern Hemisphere.  My seventh grade “Earth Sciences” teacher Mr. White told me this.  Lisa Simpson confirmed it.  I saw it reflected serenely each morning in the face of the Porcelain Goddess.  And now I have been informed over a plate of mediocre lasagna and awesome pumpkin pie that it’s all a big fabrication. 

Iceland Coriolis

(Note: the water in my toilet and the events in this picture are entirely uncorrelated)

Is it shocking that my middle school teacher got it wrong?  Not so much.  Do I really care which way the water goes down the drain?  Not in the least.  Do I feel like this is another reason for disbanding all academic institutions and preaching education from the street corners?  Yeah, a bit.

This reminds me of when my friend Jasmine found out that islands don’t float.


Posted by on December 4, 2006 in Alchemy


What Big Eyes You Have

From the potential ban on trans fats in New York city, to television personalities who constantly obsess over food, it’s clear that we are a nation with issues about how we get our nutrition.  I know I spend about half of my waking hours thinking about where and when my next meal will be (which is ridiculous, considering how easily I come by my meals).  In light of how much we consciously think about food, it’s interesting to consider how pervasive subconscious processes affect our eating habits.

In a recent interview published at Salon, Brian Wansink of the Cornell University Food and Brand Lab discusses how our brains and our bodies negotiate to decide when we should stop eating.  He describes some of the cues in each meal that tell us to keep going whether we like it or not.

We set these cues up for ourselves (or our hosts do it for us); factors such as table arrangement, plate size, our company at the table, where we store our food, and others all affect how much we choose to eat.  Wansink describes one striking example of subjects who ate more despite being thoroughly educated about the affect of eating from a larger bowl:

So, as an experiment, we took a bunch of really intelligent people — MBA graduate students at the University of Illinois at Urbana-Champaign — competitive students who had gotten into graduate school. I spent 90 minutes informing them that if they serve from a big bowl, they’re going to take more than if they serve from a medium bowl. I demonstrated it. I lectured about it. I showed them a video about it. I even broke them into discussion groups so that they could discuss ways they could prevent it from happening to them. I did everything short of an interpretive dance.

Then, they went away for a holiday break. When they came back I invited them to a Super Bowl party at the end of January, six weeks later. As they came to the party they went to one of two rooms. In one room, they were given a bowl, but sitting in front of them was two large, gallon bowls of Chex Mix. Then, they served themselves, and we weighed how much they’d taken. 

We did this in a very sneaky way. We handed them something that they had to fill out, so they had to put their plate down, and there was a scale, concealed by a tablecloth, underneath where they put their plate. At the same time, 20 of their colleagues were going through a different room that had four medium half-gallon bowls of Chex Mix. So, instead of large bowls they served from medium-size bowls, but it’s the same total volume of Chex Mix.

When people served themselves from the huge bowls, they served themselves 53 percent more Chex Mix. Now, these were smart people and they were very well informed. In fact, six weeks earlier we’d spent 90 minutes drilling them over and over and over again about how big bowls cause you to pour more. So, after the Super Bowl was over we weighed how much they’d actually eaten, and the people who served from the huge bowls ate 57 percent more.

When we said, “Hey, here’s what’s happened. We told you guys about this six weeks ago, why did you get fooled?” people were still unwilling to say that the size of the bowl fooled them. They’ll deny it until they’re blue in the face. They say: “Oh, well, yeah, I was really hungry today,” or “I skipped lunch,” or “It smelled really good.” They’ll say anything but that bowl could have possibly influenced them.

Our eyes really may be bigger than our stomachs, and that does not bode well for a nation continually feeding the reaper with its incessant addiction to food. 

In another example of super-sneaky research, Dr. Wansink describes serving subjects in “bottomless soup bowls” that discretely refill as soon as they are half-empty.  It turns out that people eating from these bowls tend to keep eating just because there is still soup there; and they don’t just eat a little more; we’re talking as high as 73% more soup. 

A lot of this has been known for a long time, but Wansink is adding a quantitative backbone to the ideas.  Restaurants could easily take advantage of these results to help people eat more reasonable portions, but they won’t, because they’re much happier taking advantage of the results to help people eat hugantic portions.

 Thanks to Garnet for the link.


Posted by on December 4, 2006 in Alchemy


Giant Microbes

GIANTmicrobes is a company that makes stuffed replicas of a wide variety of virii, bacteria, and other bugs at millions of times their actual size.  Today might be a good day to purchase one from their “professional series” for HIV.

GIANTmicrobes HIV

Thanks to Phoebe for the link.

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Posted by on December 1, 2006 in Alchemy, Entertainment


Please Use a Condom

Please Use a Condom

Fox wears a ribbon for World AIDS Day.

Support World AIDS Day

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Posted by on December 1, 2006 in Photos