Friday, April 29, 2005


Last Friday after getting home from work, I discovered that Rem, the mother of our six baby mice, had died.

Rem: ~2004 to April 22, 2005

We first met Rem in October of last year, when she took part in a metabolic rate experiment in my lab. We noticed she was pregnant, and brought her home so she could give birth in peace. She quickly charmed us into making her a member of the family, spawning a long series of blog posts in the process.

Back in January Rem fell ill, but quickly recovered, and had been doing fine since then. Even the day before she died, Rem appeared healthy and attentive, and was chewing on the cage as usual.

I found Rem already dead, lying on her side in the bedding. There were no injuries, her fur was clean and well-groomed, and she was as plump as ever. I have no idea why she died.

Here's to the mouse who opened my eyes to mice, and who trusted us to handle her babies while she hunted for sunflower seeds in the egg-carton maze on our dining room table.

Mom mouse playing

Still busy ...

While I've finished most of my non-teaching related work for the semester, I still have stacks of weeks-old papers that need to get graded this weekend. And, in the category of "couldn't I have scheduled this for any other weekend?", I have to run field labs both Saturday and Sunday. So, blogging will stay light for a bit.

However, I have some sad news that I've delayed posting too long already, so that will be coming up shortly.

Tuesday, April 26, 2005

The grant is in!

We submitted our grant to the NSF this afternoon, getting it in 2.75 hours before the deadline; it was 38 pages long (including the forms auto-filled in by the NSF and a few nearly blank pages). Many thanks to Semantic Compositions, who read over a few near-final drafts late last night and made some excellent suggestions.

In other news, the interviews are now over, and I've also finished the building equipment list.

I'm exhausted. I'm going to go collapse on the couch and listen to some George Sarah while doing absolutely nothing (besides the various regulatory activities required to maintain my resting metabolic rate).

More later.

Friday, April 22, 2005

Light blogging

Regular readers have probably already noticed the relatively light blogging of the last few weeks; the primary cause has been my involvement in too many (interesting but time consuming) committees and projects on campus.

Unfortunately, almost every project I'm working on has something major due in the next few days, so blogging will probably stop until some time next week. I have to be in interviews all day today and tomorrow, for a total of 12+ hours over the two days. I have to make a full list of all the equipment needed in my labs in the new building we're designing; the building won't be built for at least 5 years, but they still need the list by today (and only formally asked for it last week). The drop date for classes is next week, and I have a huge stack of papers my students need to get back so they can decide if they need to drop. And, topping it all off, my NSF grant application is due next week.

So, that's it for now. Have fun all.

LA Times - education

George Skelton has a column in the LA Times with the encouraging title of The Governor Owes Schools an Apology -- and $2 Billion.

The article focuses on the proposition 98 debate, and is a good summary of the issues that are at least partially behind the severe budget problems at many campuses statewide. It also includes more detail about last year's (now broken) promise to fully fund proposition 98:
"Schwarzenegger was desperate for money, and school officials wanted to cozy up to the charismatic, larger-than-life new governor. Also, they feared a worse result if there was no cooperation. So they agreed not to fight for the $2 billion on the condition that it be returned -- that is, returned to their guaranteed annual funding base. It hasn't been.

"The governor assured schools that if tax revenues increased this year, he'd give them their normal cut under Proposition 98. Revenues did, but he didn't.

The final paragraph of the statement Schwarzenegger released at the deal's announcement read: 'This Prop. 98 funding will be restored as required by law and our agreement. Today, I am making that promise to our teachers and students.'

"Schwarzenegger didn't just renege on the deal. He's pushing a budget 'reform' to amend Proposition 98 so that repayment of back money owed schools -- roughly $4 billion -- is stretched out over 15 years and not added to the guaranteed base.

Wednesday, April 20, 2005

Tangled Bank #26

Tangled Bank Blutton
The one-year anniversary edition of the Tangled Bank has now been posted at Circadiana.

Well that's just great.

We've made a lot of progress on the NSF grant a few of us are applying for. I now have FastLane access, and last week we finalized the list of proposed activities for the grant. We worked out a rough budget, with justifications, and last night I was on campus until 12:45 am writing descriptions of our proposed activities. I decided that it would be best to check whether all of our proposed activities were actually fundable with the grant (since the grant description was a bit vague), so last night I sent a summary of our proposal to the grant's NSF contact.

I'm glad asked. More than half of our proposed budget items do not quality for funding, and should be "supported separately". Luckily, we had a meeting already scheduled for today, so we were able to salvage a lot and decide on some new plans, but that e-mail sure was a lousy way to start the day.

Tuesday, April 19, 2005

Tangled Bank Announcement

Tangled Bank Blutton
The one-year anniversary edition of the Tangled Bank will be posted this Wednesday at Circadiana. Get your submissions in by tonight to "coturnix1 AT aol DOT com", or to, if you want to be included.


I have updated the strawberry shortcake recipe. The original post incorrectly included 1 tablespoon baking soda; the recipe actually uses 1 tablespoon baking powder. I apologize for any confusion (or badly baked shortcake).

I wonder how much of a difference it makes.

Monday, April 18, 2005

Garlic and clam cream sauce pasta

My SO and I found this recipe in an issue of Fine Cooking a few years ago, and since then it's been one of our most frequently-made recipes. The sauce is not as thick as your typical cream sauce (e.g., fettuccine alfredo), and is also quite flavorful thanks to the combination of clams, garlic, herbs, and cheese.

This recipe is quick and easy; my SO and I can make this dish in less than 25 minutes. The slowest step is cooking the pasta, and even that can be done in parallel with making the sauce. Since I made this last week after a long day at work, it's this week's end-of-the-week recipe blogging post.

1 1/2 tablespoons butter
2 6.5oz cans chopped clams (drained, reserve the liquid for the juice below)
3 large cloves garlic, finely chopped or pressed with a garlic press
1/2 teaspoon dried oregano
1/4 teaspoon red pepper flakes
2/3 cup clam juice (reserved from the cans above)
1/2 to 2/3 cup heavy cream
1/4 cup chopped fresh parsley
1/4 cup grated Parmesan or Pecorino Romano cheese
1/2 pound dry pasta (we often use fusili)

0. Cook the pasta in salted water until it is al dente. When cooked, drain the pasta, but do not rinse with water. Work on the sauce (steps 1-6) while the pasta is cooking, though try to schedule your cooking so the pasta is done somewhat before it needs to be added to the sauce (in step 8).
1. In a large frying pan melt the butter over medium-high heat.
2. Add the clams and fry for 1-2 minutes, stirring frequently.
3. Add the garlic and fry for a minute longer, stirring frequently.
4. Add the oregano and red pepper flakes, stir for a few seconds, and then add the clam juice.
5. Cook until the clam juice is reduced in volume by approximately 50% (a few minutes).
6. Add the cream, and cook (simmering) until the sauce is a good consistency to coat the pasta (a moderately-thick sauce), stirring occasionally. It usually takes 2-4 minutes for the sauce to thicken to the right consistency; check the thickness of the sauce by stirring regularly with a spoon. When ready, the sauce should be a good deal thicker than it was just after you added the cream.
7. Once the sauce is thickened, mix in the parsley and cheese.
8. Add the drained pasta, mix well, and serve with grated cheese.

This recipe makes enough for a hearty dinner for the two of us, with very little left over. The original article says that the pasta doesn't reheat well; I've found that it reheats just fine in the microwave, as long as I mix it frequently as I reheat it, and add a little bit of freshly grated cheese once it's hot.

The flavor of the sauce is much more intense if you use fresh parsley, so don't use dried parsley unless you absolutely have to. Parsley is pretty easy to grow; I have a parsley plant in my backyard that I use primarily to make this dish.

The original article encourages flexibility with the sauce's ingredients, and includes five other recipes for similarly flavorful cream sauces.

Weinstein, B., and M. Scarbrough. 2002. "How to Make a Light Creamy Pasta Sauce." Fine Cooking 50: 45-49.

Sunday, April 17, 2005

Learning Perl

This weekend I've been trying my hand at revising some of TWiki's code, which is written in Perl. Before today I'd never worked in Perl, so I spent most of my time learning the basic syntax, but thanks to a number of online references I was able to make the changes I wanted. Here are the sites that were of particular use:
Of course, I didn't find until after I'd done most of my work. They have a very nice beginners area, which includes links to four online textbooks that are free to read online.

Alternative Medicine and Autism

Autism Watch, a sub-site of, is dedicated to taking a skeptical look at autism treatments. The editor, a scientifically-minded MD, has posted Through the Looking Glass: My Involvement with Autism Quackery, an article describing how he was seduced by alternative treatments for the disease, only to realize that all the alternative treatments he was trying were ineffective. Here's part of the conclusion:
"Looking back on my experiences with 'alternate' autism therapies, they seem almost unreal, like Alice's adventures in Wonderland. Utter nonsense treated like scientific data, people nodding in sage agreement with blatant contradictions, and theories made out of thin air and unrelated facts -- and all of it happening right here and now, not in some book. Real people are being deceived and hurt, and there won't be a happy ending unless enough of us get together and write one."

You know you're a geek when ...

your idea of a fun evening is spending the few precious non-work hours you have fiddling with TWiki, in an attempt to add a couple of new functions.

Thursday, April 14, 2005

Appendices and caeca

This morning I got an e-mail from the significant other of one of my students, informing me that said student would be missing class because he had just had his appendix removed. I sent back my standard reply "too bad, come to class or you fail" "Don't worry about missing class, take care of yourself, and we'll worry about this later," but since the comparative anatomy and physiology of the appendix is so cool, I thought I'd give my student something to enjoy while he was recovering. Thus, I sent his significant other this letter:

You should tell him [my ill student] that what the doctor removed was functionally a vestigial caecum.

He'll probably remember that we've talked about different methods herbivores use to digest cellulose (ruminants with symbiotic bacteria in their rumens, termites with symbiotic bacteria in their guts, leaf-cutter ants farming cellulose-digesting fungi), but one method used by animals to digest cellulose I left out of my lecture is a structure called the caecum.

A caecum is a blind-ended pouch that is attached to the digestive tract just between the small intestine and the large intestine. In herbivores that use caeca to digest cellulose, the caecum is quite large, and cellulose-rich food gets diverted into the caecum after it's passed through the small intestine. Inside the caecum, symbiotic bacteria digest the cellulose; once the cellulose is digested into glucose, it is moved out of the caecum and back into the large intestine.

Unfortunately, the large intestine doesn't do any absorption of nutrients (that's what the small intestine does), so all that digested cellulose just passes right through the large intestine, and then out of the body, without being absorbed. So, animals that have a caecum typically practice coprophagy, consumption of their own feces. They actually produce two types of fecal pellets: one that's just the standard waste (that they don't eat), and one that's primarily composed of nutrients from the caecum (which they do eat). After reingesting the digested cellulose, they absorb it as it passes through their small intestine. Rabbits digest cellulose using a caecum and coprophagy, as do a number of other non-ruminant herbivorous mammals.

Humans don't have an enlarged caecum, but we do have a very small pouch where a caecum would be, and we call it the appendix. It has very little function in us (since it's not big enough to house large populations of symbiotic bacteria), other than giving us appendicitis. It's a little "gift" from our evolutionary ancestors who did have a caecum ...

[Ed. note: yes, I'm using the British spelling of cecum. I think it looks cooler. And apparently the appendix does play some role in the immune system, so it's not completely without function.]

Tuesday, April 12, 2005

Lentils with cumin and garlic

My SO is currently in London staying with family, and called over the weekend to report that they have an emergency: they have two full bags of lentils that need to be eaten in less than two weeks. My SO wanted me to send some lentil recipes, so, without further ado, here is my solution to the lentil crisis of 2005. Since I cooked this for dinner Sunday night, this will also be last week's (slightly delayed) end-of-the-week recipe blogging post.

1 1/2 cups dry lentils (yellow or pink)
3/4 teaspoon ground turmeric
5 cups water
2 teaspoons kosher salt
1/4 cup vegetable oil
1 teaspoon cumin seeds, whole (optional)
6 large cloves garlic, thinly sliced

1) Rinse the lentils, and check for any stones mixed in.
2) Put the lentils, turmeric, and water into a pot. Stirring occasionally, bring the water to a boil, and simmer, partially covered, until the lentils are soft throughout. For yellow lentils this will be ~40 minutes; for pink lentils this will be ~25 minutes (or check the suggested cooking time on the package of lentils you have).
3) Remove the lentils from the heat and stir in the salt. Mix the lentils vigorously with a whisk or spoon, or mash with a potato masher, until the lentil mixture is slightly creamy. You should have approximately 5 cups, and it should be similar in consistency to a thick cream soup. Thin with additional water if necessary.
4) Heat the oil in a frying pan over medium heat.
5) When the oil is hot, add the cumin seeds and fry for about a minute, then add the garlic slices and cook until the garlic just begins to turn brown, approximately 2 minutes.
6) Pour the oil, garlic, and cumin into the cooked lentils, stir well, and serve.

This recipe is extremely simple, yet tastes marvelous; the flavors of the fried cumin and garlic permeate the turmeric-laced lentils, and your guests will never know that there were only four main ingredients (excluding oil, water, and salt).

This recipe is slightly modified (reduced oil) from Sahni's "Classic Indian Cooking".

Sahni, Julie. 1980. Classic Indian Cooking. William Morrow & Co, NY. pp. 332-333.

Monday, April 11, 2005

Grant writing

My two time-sucking committees have finally relaxed a bit; I won't have another major commitment due to them until late next week. Unfortunately, this gives me the perfect bit of time to finish working on an NSF grant that I and a few other science faculty are applying for. It's due in a few weeks and, of course, I volunteered to coordinate the application process.

First, a little background. Faculty at community colleges are not expected to do research; all of our time is expected to be devoted to teaching and other service activities (*cough* committees *cough*). There is no research component involved in obtaining tenure at most community colleges. But, faculty are free to apply for grants if we want, and if we want to have any kind of research program, or involve students in research, we need to get grants to fund it. Since I've got a whole heap of students who are interested in doing some field research, and my campus has a neat opportunity to carry out the research, it makes sense to apply for the grant.

This is only a relatively small grant (<$30,000; the primary component is funding planning for a larger grant we'll apply for next year, if all goes well), but it's a big time commitment nonetheless. It's my understanding that most universities have staff members dedicated to helping faculty apply for grants; my college has nobody to help, and I'm not even sure in which decade the last NSF grant was awarded to our biology department. Thus, I got to spend today wading through such fun documents as the NSF Grant Proposal Guide, the FastLane instructions, and Circular A-21.

Even simple things like getting access to NSF's FastLane application system are harder than they should be. To get a FastLane account, I need to contact the "Authorized Organizational Representative" at my campus; unfortunately, said "Authorized Organizational Representative" no longer works here. I also have no idea if my campus has filed all the various institutional paperwork required by the NSF.

To give you an idea of how rarely we apply for grants like this, the president of my college is personally assisting me with the application. It's exciting that the president is gung-ho about the grant, but it's odd to be getting personal e-mails from him, and I'm definitely not used to scheduling lunch meetings with him.

Some day, maybe, I'll actually get back to spending my time on teaching ...

Gabe's art walkthrough

Gabe, the artist behind Penny Arcade, has posted a step-by-step walkthrough of how he drew his latest CTS (Cardboard Tube Samurai) print, from pencil sketch to final image. Go and enjoy; it makes a very nice distraction from grant writing.

Saturday, April 09, 2005

Adding a hard drive to the Debian box

Tonight I installed a new hard drive in my Debian 3.1 box, primarily so I could move the /var directory from it's old location in the root partition of the primary drive to a new, much larger, partition on the new drive.

While the Debian documentation has good information on partitioning and formatting hard drives, it had relatively little information on migrating system data from one drive to another. I found three good sites that helped me get through the process:

I didn't find any resources online that specifically walked me through how to move /var, so I integrated the pages' advice and gave it a go. Here's what I did (as with my prior Debian posts, if you're looking for help, remember that I'm a complete novice):
  1. I backed up all my critical data, including the entire /var directory, and then installed the new drive into the machine.
  2. I determined that the new drive was /dev/hdb (done by "cat /proc/partitions").
  3. I used "cfdisk /dev/hdb" to partition the drive and "mkfs /dev/hdb1" to format the new partition.
  4. I entered single-user mode by running "init 1" from the console.
  5. I mounted the new partition to /mnt/hdb1 (first creating the directory /mnt/hdb1, then using "mount /dev/hdb1 /mnt/hdb1").
  6. I copied everything in /var to the new drive, using "cp -pr * /mnt/hdb1" from the /var directory.
  7. After verifying that everything seemed to be OK, I added a line to /etc/fstab so the new drive would be mounted as /var. The line was "/dev/hdb1 /var ext2 defaults 1 2"
  8. I renamed /var to /var-old ("mv /var /var-old"), created a new, empty, /var directory, and then ran "mount -a" to mount the new drive based on the fstab line.
  9. I exited single user mode ("exit"), and that was it!

I was impressed with how relatively easy the entire process was; it took less than half an hour from start to finish, not including research time. Now that I've got the drive mounted, the transition from one hard drive to the other is completely seamless; /var looks and acts like any other directory, yet it's on a completely different physical drive.

Ah, the wonders of Linux.

Friday, April 08, 2005

More Community College Budget Woes

My dad forwarded me another article about the current California community college budget issue. The article, Science Students Beg for Classes (registration required; in the San Jose Mercury News), reports that Mission College's new science building isn't being used to its full potential due to a lack of funding for classes.

The scenario at Mission College sounds very similar to what is happening at my campus; there is high demand for many courses, but not enough funding for equipment and technical staff to allow those sections to run.
"Microbiology now fills up the fastest [of the college's health-related courses], but is also the most expensive course, said instructor Jean Replicon.

"'We have one lab dedicated for microbiology that is being used 10 hours a week,' Replicon said. 'We could use it all day and evening and weekend.'

"Compared with an English class, for which the college has to purchase minimal supplies, offering courses such as microbiology, physiology and chemistry is expensive. The college must buy everything from microscopes, biological specimens and cultures to beakers and chemicals.

"Also critically important are skilled lab technicians who perform such tasks as preparing media and cultures so experiments work.

"The college has money to hire additional instructors, especially for classes that are guaranteed to fill, said Jim Burrell, chairman of the division of general sciences. But there is no money for supplies and more technician time.

"Replicon said it would cost $17,500 a year to offer one new section of microbiology each semester -- just for the materials and technician staffing. She estimates there is enough student interest to fill four or five more sections.

"The need for equipment is another obstacle. Without a bigger sterilizer, called an autoclave, it would be difficult to add more microbiology sections, Replicon said. A new one would cost $25,000, but the money is not there.
A notable difference between Mission college's scenario and ours is that Mission college's dean reports that they have money to hire new instructors, as long as the new classes will fill. I've never heard that from the administrators at my campus.

To help cover the cost of expensive courses like microbiology, many California community colleges used to charge an equipment fee (separate from tuition) when a student registered for a course like microbiology. While this seems logical, the state has recently cracked down on equipment fees, mandating that, among other things, the students must be able to keep whatever equipment is bought with their equipment fees. Since colleges clearly cannot let students take home their bacterial cultures, or their formaldehyde-preserved specimens, this new restriction functionally eliminates the possibility of using equipment fees to help with such programs.

So, at least at my campus and at Mission college, we're left with programs that have high student demand, and even faculty available to teach the courses, but no money to offer the courses, and thus scores of students get turned away every semester.

Thursday, April 07, 2005


I'm finally done with work for the day. Unfortunately, it's 1:00am, meaning that I've been on campus for 16 hours straight. I haven't even had a real break for meals: I had a working lunch at my desk, and ate dinner by ordering pizza for everyone in the student research-group meeting I led tonight. Yesterday was a comparatively easy 12 hour day.

I'm not alone in my long hours this week, as the dean of my division was in his office until only an hour or so ago, and many of the other faculty in the department have also been around much more than usual. Most of this departmental stress is being caused by a committee meeting scheduled for tomorrow morning.

I'd write more, but I should really go home and get some sleep.

If you're desperate for something scientific to read, check out Orac's Tangled Bank #25 post (which I haven't even read yet).

Monday, April 04, 2005

My SO departs

My SO is heading out of town tomorrow morning for a four-week trip, so tonight it's time to finish the taxes, help my SO pack, and try to spend a bit of time together relaxing and making a nice dinner.

Since tonight's for my SO, and the rest of the week will be filled with committee work and meetings (again), blogging will be light for a little while (meaning I probably won't finish my Tangled Bank post in time; sorry, Orac).

If you're desperate for something to do, go make some strawberry shortcake to tide yourself over.

Sunday, April 03, 2005

Real strawberry shortcake

Strawberries have started to go on sale in our area, so on Friday, my SO and I made one of our favorite treats, strawberry shortcake. Shortcake is a slightly sweet biscuit that goes perfectly with the sweet and tangy strawberries and soft whipped cream. Shortcake is neither sponge cake nor angel food cake nor pound cake; all of those are quite sweet, and thus don't contrast with the strawberries nearly as well as real shortcake does. If all you've ever eaten is strawberry sponge cake, strawberry angel food cake, or strawberry pound cake, you owe it to yourself to make some real strawberry shortcake. Thus strawberry shortcake is this week's end-of-the-week recipe blogging post.

In their strawberry shortcake recipe, Joy of Cooking suggests using either shortcake or sponge cake. On this important issue I must stand firm against the words of the cooking bible: strawberry shortcake should only be made with shortcake; strawberry sponge cake is an imposter that should be banished. If that makes me a cooking heretic, than so be it.

There's no reason to buy anything pre-made for this recipe, except possibly whipped cream in a can (e.g. Reddi-wip). While grocery stores sell gallons of strawberry glaze, all you have to do is add sugar to sliced strawberries, and osmosis will kindly make the glaze for you, drawing out moisture from the strawberries to create a sweet syrup. Making the shortcake from scratch is as easy as making biscuits; the only useful piece of specialized equipment is a pastry blender, but even that can be replaced with two knives, a fork, or your fingers.

2 cups flour
1 tablespoon baking powder
1 tablespoon sugar
3/4 teaspoon salt
6 tablespoons cold unsalted butter
3/4 cup milk or half-and-half

Strawberry topping:
2 pint fresh, whole strawberries
1/2 cup sugar (or to taste)

Sweetened whipped cream (homemade or canned, e.g. Reddi-wip)

To prepare the strawberries:
1) Rinse the strawberries and remove the calyx (sepals).
2) Slice the strawberries lengthwise 1/8 to 1/4 inch thick and place into a bowl.
2) Add the sugar to the strawberries and mix well.
3) Let the mixture sit at room temperature for at least 10-15 minutes, stirring occasionally.

To make the shortcake:
0) Preheat your oven to 450F.
1) Mix the flour, baking soda, sugar, and salt in a large bowl. I typically use a pastry blender to do this, though a fork or whisk also work.
2) Cut the butter into a few pieces and add to the flour mixture. Use a pastry blender, fork, knives, or your fingers to cut the butter into the flour, stopping when the largest chunks of butter are pea-sized and most of the butter is in very small pieces. Be careful not to melt the butter.
3) Add the milk or half-and-half, and mix with a spoon until the dough starts to come together. Knead the dough against the sides of the bowl a few (~5) times. If the dough doesn't come together easily, even after kneading, try adding a tablespoon or two more milk or half-and-half.
4) Roll or pat the dough out on a floured work surface until it is approximately 3/4 inch thick.
5) Cut the dough into 2 1/2 to 3 inch squares. I don't worry if they're not perfect squares; I just cut the pieces so I use all the dough. If you want a more formal presentation, you can cut the pieces into perfect squares or use biscuit cutters, and then re-roll the leftover pieces to use them.
6) Bake, on a cookie sheet, in a 450F oven for 10-12 minutes, or until the tops are moderately browned.
7) Let the shortcakes cool a minute or two before serving.

Assembling the shortcakes:
1) Split a shortcake horizontally (a fork can help) and place the halves, interior facing up, onto a plate. Spoon strawberries and accumulated syrup onto the top of the shortcake, top with lots of whipped cream, and enjoy.

Here's what ours looked like on Friday:
Strawberry shortcake

Two pints of strawberries allow for a very generous proportion of strawberries to shortcake; you can make this with only one or one and a half pints of strawberries (scaling down the sugar) and still be fine. Keep in mind that as water leaves the strawberries to make the syrup, the strawberries will start to soften. Thus I generally try to prepare only as many strawberries as will be consumed in one sitting, though if you like softer strawberries (as my SO does), you can prepare them ahead of time and put them in the refrigerator until you need them.

We typically use the pre-made sweetened whipped cream that is available in the dairy section of most grocery stores, primarily because it's more convenient than whipping fresh cream by hand and tastes similar to freshly whipped cream. If you prefer homemade whipped cream, by all means use it instead of the canned variety. Joy of Cooking suggests that whipped cream mixed with sour cream makes a good topping; we've used that mixture on tarte tatin and loved it, but we've never tried it on strawberry shortcake. Please don't use Cool Whip.

The shortcake recipe is slightly modified from Joy of Cooking.

Rombauer, I. S., M. R. Becker, and E. Becker. 1997. Joy of Cooking. Scribner, NY.

Academics in South Park

PZ Myers has also depicted himself in South Park form, using South Park Studio v2.0, and so have a number of other academics. Here's a catalog of what I've found so far:

PZ Myers
Yowling from the Fencepost
The Dubious Biologist
Alex Merz
De Rerum Natura
Me (Radagast)

First observation: stubble. I guess most academics don't shave.
Second observation: glasses.

I'll be happy to add anyone else to the list.

Additions to the list:
David Winter

Saturday, April 02, 2005

Radagast at mid-semester

My SO used South Park Studio v2.0 to make a South Park version of me:

Radagat as a South Park character
Radagast + mid-semester = stress

This representation is distinctly less heroic than my hero avatar. The bags under the eyes are a nice touch. And yes, I do need to shave and get a haircut. Can I have another week off?

Statistical analysis of 2004 presidential election exit polls

USVoteCounts, a "scientific research project whose mission is to objectively investigate the accuracy of elections in America" has published a paper reporting on the discrepancy between exit polling and vote counts in the 2004 presidential election. The paper is titled "National Election Data Archive Project Analysis of the 2004 Presidential Election Exit Poll Discrepancies" and is authored by a number of statisticians and mathematicians; it's available as a full-text PDF and an executive summary PDF.

The abstract is a good summary (as it should be):
"What is the Main Cause of the Discrepancies between the Official Election Results and the Exit Polls?

"The exit pollster of record for the 2004 election was the Edison/Mitofsky consortium. Their national poll results projected a Kerry victory by 3.0%, whereas the official count had Bush winning by 2.5%. Several methods have been used to estimate the probability that the national exit poll results would be as different as they were from the national popular vote by random chance. These estimates range from 1 in 959,000 to 1 in 1,240. No matter how one calculates it, the discrepancy cannot be attributed to chance.

"Edison/Mitofsky disavowed the results of their own poll, saying that the data cannot be construed as evidence that the official vote count was corrupted, and hypothesized that Kerry voters were more amenable to completing the poll questionnaire than Bush voters. However, Edison/Mitofsky's own exit poll data does not support their theory that a higher exit poll response rate by Kerry voters accounted for the discrepancies between the exit polls and the presidential election results. Using Edison/Mitofsky’s data tables we demonstrate that the “reluctant Bush responder” hypothesis is implausible because it is inconsistent with the combination of high response rates and high discrepancy rates among the precincts with the highest percentage for Bush.

"There are Three Primary Explanations for the Discrepancies:

"1. Statistical Sampling Error – or Chance
We agree with Edison/Mitofsky that the first possible cause, random statistical sampling error, can be ruled out.

"2. Inaccurate Exit Polls
This is the theory that Edison/Mitofsky put forth. They hypothesize that the reason the exit polls were so biased towards Kerry was because Bush voters were more reluctant to respond to exit polls than Kerry voters. Edison/Mitofsky did not come close to justifying this position, however, even though they have access to the raw, unadjusted, precinct-specific data set. The data that Edison/Mitofsky did offer in their report show how implausible this theory is.

"3. Inaccurate Election Results
Edison/Mitofsky did not even consider this hypothesis, and thus made no effort to contradict it. Some of Edison/Mitofsky's exit poll data may be construed as affirmative evidence for inaccurate election results. We conclude that the hypothesis that the voters’ intent was not accurately recorded or counted cannot be ruled out and needs further investigation.

Unfortunately, Edison/Mitofsky are not releasing the full precinct-by-precinct exit poll dataset for analysis, which is ridiculous considering the importance of the issue.

The closing summary of the article makes a number of very powerful points:
"There is already a strong case that there were significant irregularities in the presidential vote count from the 2004 election. Nevertheless, critics are asking for firmer proof before going forward with a thorough investigation. We feel strongly that this is the wrong standard. One cannot have proof before an investigation.

"In fact, the burden of proof should be to show that the election process is accurate and fair. The integrity of the American electoral system can and should be beyond reproach. Citizens in the world’s oldest and greatest democracy should be provided every assurance that the mechanisms they have put in place to count our votes are fair and accurate. The legitimacy of our elected leaders depends upon it.

"Well-documented security vulnerabilities and accuracy issues have affected voting equipment as far back as the late 1960s, and history shows that partisan election officials have long possessed the power to suppress and otherwise distort the vote counts. The recent and ongoing proliferation of sophisticated computerized vote recording and tallying equipment, much of it unverifiable and hence "faith-based", dramatically augments the opportunities for wholesale and outcome-determinative distortions of the vote counting process. That the lion's share of this equipment is developed, provided, and serviced by partisan private corporations only amplifies these serious concerns. The fact that, in the 2004 election, all voting equipment technologies except paper ballots were associated with large unexplained exit poll discrepancies all favoring the same party certainly warrants further inquiry.

"The absence of any statistically-plausible explanation for the discrepancy between Edison/Mitofsky’s exit poll data and the official presidential vote tally is an unanswered question of vital national importance that demands a thorough and unblinking investigation.

Friday, April 01, 2005

California Poppy Reserve

I've posted the pictures from my trip to the Antelope Valley California Poppy Reserve on my Flickr page in the CA Poppy Reserve set.

While the parking lot was packed, and there were dozens of people on the paths directly adjacent to the visitor center, once we started hiking onto the longer trails, the people disappeared:

Trail to a vista point

Hiking down that trail to the Antelope Butte Vista Point (the furthest point from the visitor center) got us a gorgeous view of this wildflower-covered hill:

Flower covered hill

We were able to soak in that view as we had a quick snack on the trail; nobody else came out to the vista point the entire time we were there. Our meal wasn't quite as romantic as it might seem, however, since the winds were very strong, and very constant, so were both cold and frantically trying to hold onto everything that might blow away (including my SO's hat).

The primary flowers we saw were goldfields, California poppies, and lupines, though there were a number of other flowers around, including a very neat white one:

Goldfields, poppies Cluster of poppies White flower

There were also a lot of beetles, caterpillars, and other terrestrial insects out and about, but relatively few flying ones due to the high winds; we didn't see a single bee, despite the abundant flowers. As we were walking along the nearly empty trails we spotted a dozen or so lizards, including one patient enough to let me get a good closeup:

Lizard at the poppy reserve

I have more pictures in the CA Poppy Reserve set on Flickr, if you're interested.

Fred Korematsu

The LA Times has a detailed obituary for Fred Korematsu, an American citizen who fought the internment of those with Japanese ancestry during World War II. Mr. Korematsu's parents were Japanese, and after not turning himself in to be interned in 1942, he was arrested and convicted of a felony charge. Mr. Korematsu's case eventually made it to the Supreme Court in 1944, where the court upheld his conviction and internment.

The 1944 Supreme Court decision (which a few judges dissented with, thankfully) is a frightful read:
"To cast this case into outlines of racial prejudice, without reference to the real military dangers which were presented, merely confuses the issue. Korematsu was not excluded from the Military Area because of hostility to him or his race. He was excluded because we are at war with the Japanese Empire, because the properly constituted military authorities feared an invasion of our West Coast and felt constrained to take proper security measures, because they decided that the military urgency of the situation demanded that all citizens of Japanese ancestry be segregated from the West Coast temporarily, and finally, because Congress, reposing its confidence in this time of war in our military leaders-as inevitably it must-determined that they should have the power to do just this."
The case was reopened in the 1980s, and Mr. Korematsu's conviction was overturned in a 1984 US District Court decision. The conclusion of Judge Patel in that decision is excellent:
"As historical precedent it [the Korematsu case] stands as a constant caution that in times of war or declared military necessity our institutions must be vigilant in protecting constitutional guarantees. It stands as a caution that in times of distress the shield of military necessity and national security must not be used to protect governmental actions from close scrutiny and accountability. It stands as a caution that in times of international hostility and antagonisms our institutions, legislative, executive and judicial, must be prepared to exercise their authority to protect all citizens from the petty fears and prejudices that are so easily aroused."