Tuesday, May 31, 2005

Grades are in!

The spring 2005 semester is now officially complete. Yay!

Cheney responds to Amnesty International

Dick Cheney was interviewed on Larry King Live yesterday, and in the interview Cheney responded to the recent Amnesty International claims that the US is violating human rights:
KING: Amnesty International condemns the United States. How do you react?

D. CHENEY: I don't take them seriously?

KING: Not at all?

D. CHENEY: No. I -- frankly, I was offended by it. I think the fact of the matter is, the United States has done more to advance the cause of freedom, has liberated more people from tyranny over the course of the 20th century and up to the present day than any other nation in the history of the world. Think about what we did in World War I, World War II, throughout the Cold War. Just in this administration, we've liberated 50 million people from the Taliban in Afghanistan and from Saddam Hussein in Iraq, two terribly oppressive regimes that slaughtered hundreds of thousands of their own people. For Amnesty International to suggest that somehow the United States is a violator of human rights, I frankly just don't take them seriously.

KING: They specifically said, though, it was Guantanamo. They compared it to a gulag.

D. CHENEY: Not true. Guantanamo's been operated, I think, in a very sane and sound fashion by the U.S. military. Remember who's down there. These are people that were picked up off the battlefield in Afghanistan and other places in the global war on terror. These are individuals who have been actively involved as the enemy, if you will, trying to kill Americans. That we need to have a place where we can keep them. In a sense, when you're at war, you keep prisoners of war until the war is over with.

We've also been able to derive significant amounts of intelligence from them that helped us understand better the organization and the adversary we face and helped us gather the kind of information that makes it possible for us to defend the United States against further attacks. And what we're doing down there has, I think, been done perfectly appropriately. I think these people have been well treated, treated humanely and decently.

Occasionally there are allegations of mistreatment. But if you trace those back, in nearly every case, it turns out to come from somebody who had been inside and been released by to their home country and now are peddling lies about how they were treated.
(from the CNN rush transcript)
Let's summarize Cheney's responses to the Amnesty International accusations:

1) I'm offended.

2) The US has done lots of good things.

3) The administrations we overthrew did lots of bad things.

4) We're at war, so we have to keep prisoners of war.

5) These prisoners have given us lots of information.

6) I think we're treating people well.

7) The allegations are only coming from people who have been released. They are liars.

Most of these responses have absolutely nothing to do with the statements made by Amnesty International that human rights violations are occuring in Guantanamo Bay, Iraq, and Afghanistan. Let's deal with them one at a time:

1) This has nothing to do with the issue (of course he's offended, they're accusing his administration of crimes).

2) Doing good deeds does not excuse criminal behavior.

3) Just because someone else does bad things doesn't mean you can do bad things too.

4) Being at war may justify imprisonment of certain persons, but does not justify torture or other cruel treatment.

5) The ends do not justify the means.

6) This is a somewhat relevant point, yet he provides no evidence for his belief.

7) That allegations of misconduct come primarily from released persons should not be surprising, since accusing your captors of misconduct is unlikely to elicit positive reactions from them. While it's possible the accusers may be lying, Cheney provides no evidence that they are.

Later in the interview Cheney says that we'll be out of Iraq by the end of Bush's term, and that the insurgency is in its "last throes":
KING: When do we leave?

D. CHENEY: We'll leave as soon as the task is over with. We haven't set a deadline or a date. It depends upon conditions. We have to achieve our objectives, complete the mission. And the two main requirements are, the Iraqis in a position to be able to govern themselves, and they're well on their way to doing that, and the other is able to defend themselves, and they're well on their way to doing that. They just announced that in the last day or two here, there've been stories about a major movement of some 40,000 Iraqi troops into Baghdad to focus specifically on the problem there.

KING: You expect it in your administration?

D. CHENEY: I do.

KING: To be removed. It's not going to be -- it's not going to be a 10-year event?

D. CHENEY: No. I think we may well have some kind of presence there over a period of time. But I think the level of activity that we see today, from a military standpoint, I think will clearly decline. I think they're in the last throws, if you will, of the insurgency. We've had reporting in recent days, Larry, about Zarqawi, who's sort of the lead terrorist, outside terrorist, al Qaeda, head of al Qaeda for Iraq, may well have been seriously injured. We don't know. We can't confirm that. We've had reporting to that effect.

So I think we're making major progress. And, unfortunately, as I say, it does involve sending young Americans in harm's way. But America will be safer in the long run when Iraq and Afghanistan as well are no longer safe havens for terrorists or places where people can gather and plan and organize attacks against the United States.

Monday, May 30, 2005

English muffin bread

Now that the semester's functionally over, I finally have more time to cook. So, this afternoon I made my favorite bread recipe from Beard on Bread (Beard 1973): English muffin bread. English muffin bread has the texture and taste of English muffins, but is baked as a loaf; it tastes divine when cut into thick slices, toasted, and covered with butter (which fills all the nooks and crannies).

One reason I love making this bread is that it's easy. There's no kneading, and it only requires basic ingredients. All you need is a few minutes to mix up the dough, and then the yeast and oven do the rest. Making bread by hand could hardly be simpler, and thus this bread is this week's end-of-the-week recipe blogging post.

Here's what my loaf looked like today:

Loaf of bread

Toasted bread
I wish all my loaves looked like this.


1 package (1 tablespoon) active-dry yeast
1 tablespoon sugar
1/2 cup warm water (~100-115F; warm but not overly hot on your wrist)
2 1/2 cups white flour
2 teaspoons salt
7/8 cup warm milk (I heat it up briefly in the microwave)
1/4 teaspoon baking soda
1 tablespoon warm water
Butter or shortening for greasing the pans

1. Mix the yeast, sugar, and 1/2 cup warm water in a large bowl and wait for it to proof (~5 minutes; wait for the yeast to start actively metabolizing, signaled by the formation of a froth on the surface of the water). I do this in the mixing bowl of our stand mixer.
2. Mix the flour and salt in a small bowl.
3. Alternately add the flour mixture and warm milk to the proofed yeast, mixing well between each addition. I typically add about 1/4 of the flour and then 1/4 of the milk with each addition, though the amounts don't seem to be critical. We use our stand mixer with a paddle attachment for mixing (which makes the bread very easy to make), but you can also use a wooden spoon (which gives you a workout in addition to tasty bread). When finished, the dough should be a cohesive, smooth mass (that is much moister than typical bread dough), and should appear as though it's pulling away from the sides of the bowl when stirred. Do not knead the dough.
4. Once the dough is mixed, scrape the dough off the sides of the bowl with a rubber spatula, cover the mixing bowl with a moist kitchen towel, and let the dough rise until it has doubled in volume, typically 45 minutes in our kitchen (Beard suggests 1 1/4 to 1 1/2 hours; maybe he kept his kitchen much colder than ours).
5. Once the bread has doubled in volume, mix it briefly with a wooden spoon (to collapse the dough).
6. Combine the baking soda and 1 tablespoon water in a small bowl, and then add it to the dough, mixing thoroughly.
7. Transfer the dough to a greased loaf pan; I use a 11.25" x 4.5" x 2.75" pan (interior dimensions; l x w x h), which makes a long, shallow loaf, though you could use whatever size loaf pans you desire (dividing the dough between two standard 8" loaf pans works well).
8. Cover the loaf pan(s) with a piece of plastic wrap (lightly oiled to prevent the plastic wrap from sticking to the dough), and let the dough rise until it's doubled in volume (~45 minutes in my kitchen, though Beard suggests 1 to 1 1/4 hours). Don't let the dough over-rise, as it may collapse during or after baking.
9. When the bread is close to finished rising, preheat the oven to 375F.
10. Once the bread has risen, bake the bread in the preheated 375F oven until the top is a dark golden brown, approximately 30 minutes.
11. When the bread is done, remove it from the oven and place it (still in the pan) on a cooling rack.
12. After five minutes of cooling, remove the bread from the pan (sliding a knife around the edges can help release the bread), and put the bread back on the cooling rack.
13. Let the bread cool completely. This is the most difficult step of the entire recipe, as your kitchen (and house) will be filled with the scent of freshly baked bread, but you can't have any. My willpower rarely holds out until the bread is completely at room temperature.
14. Cut into thick slices, toast, and butter generously.

As a side note, regular readers may recognize that this bread served as the base for our smoked salmon eggs Benedict.

Reference:

Beard, J. 1973. Beard on Bread. A.A. Knopf, Inc, New York. pp. 156.

Back to the blogs ...

My semester is almost wrapped up; on Saturday I finished most of my grading, and with any luck I'll formally turn in my grades on Tuesday. So, today I got to spend a few solid hours surfing blogs, with no work-related distractions. Amazing. Here's some posts of note:

Sunday, May 29, 2005

Gov. Schwarzenegger digs pothole, then fills it

Gov. Schwarzenegger is trying to promote his recent decision to fund transportation (at the expense of education and other state programs). To show just how much he cares about transportation, on Thursday he staged a media event wherein he helped a road crew fill a pothole in a San Jose street.

There was only one problem: the pothole Gov. Schwarzenegger filled was dug a few hours earlier by a city work crew (reported in the SF Chronicle).
"But neighbors in the area said while they welcomed the work by the governor, they weren't sure the repairs were so critical.

"Greco, who used his video camera to record the crews ripping up his street, said Laguna Seca Way had 'a few cracks,' which he termed 'unsightly,' but they weren't as bad as the 'major potholes' a few blocks away.

"'The street was very drivable,' Vujevich said.
"
The article also discusses how the Governor has started announcing some of his appearances only a few hours in advance, most likely to help him avoid protesters (who are typically protesting for such radical causes as better support for teachers, nurses, police, and firefighters).
"The governor, asked Thursday whether the stealth schedule suggested he has been bothered by his vocal opponents, blithely dismissed them, saying most 'are paid by the unions to protest.'

"'These are all people who want to stop progress. These are all people that are fighting for the status quo ... all the people that have created the problems in the first place,' he said. 'So we don't pay very much attention to that at all. We're paying attention to millions and millions of signatures that people of California have given us in order to change the system.'
"
The charge that protestors are "paid union protesters punching the clock" has been made before (e.g., this Chronicle article on protests in San Francisco), and it seems as though the Schwarzenegger administration has no evidence for their claims.
"Union organizers denied that workers were paid to attend the protest, and Stutzman [the governor's spokesman] declined to offer any evidence of payments from the unions."
Rose Ann DeMoro, executive director of the California Nurses Association, says about the San Francisco protest,
"We didn't even do a mailing to get people here. We just talked to our members and had them call their families and friends."
So our governor ignores people who are spending their own time and money to protest to bring attention to our woefully underfunded educational system (and other state programs), and instead considers the protesters to be "the people who created the problems in the first place." Excuse me? Who's shorted education by $1.5 billion, at a time when we could desperately use the money? Who wants to destroy the retirement plans of public employees? Oh, that's right ... our governor.

Instead of hiding from the public and filling fake potholes, there's a much easier way to stop people from protesting: give our state programs the funding and support they need (and have been promised).

(via BoingBoing)

Saturday, May 28, 2005

Signatures needed on a letter to Bush

Rep. John Conyers is one of the representatives who recently sent a letter to Bush asking him to explain the leaked UK memo that states the US administration was on a course for war with Iraq long before they publicly said they were. Unfortunately, the Bush administration has not responded to the congressional letter, and so now Rep. Conyers is asking for people to sign a letter to Bush, imploring him to respond to the memo. Rep. Conyers is hoping to get more than 100,000 signatures before delivering the letter to the White House.

Rep. Conyers has posted about this in his blog, the homepage of his website has an open letter asking for assistance, and he has also posted the full text of the letter he wants people to sign here.

Why are Rep. Conyers and other people concerned about this memo? Rep. Conyers explains on his blog:
"First, the memo appears to directly contradict the Administration's assertions to Congress and the American people that it would exhaust all options before going to war. According to the minutes, in July 2002, the Administration had already decided to go to war against Iraq.

"Second, a debate has raged in the United States over the last year and one half about whether the obviously flawed intelligence that falsely stated that Iraq possessed weapons of mass destruction was a mere "failure" or the result of intentional manipulation to reach foreordained conclusions supporting the case for war. The memo appears to close the case on that issue stating that in the United States the intelligence and facts were being "fixed" around the decision to go to war.

"These are not routine questions within a partisan give and take. Under the United States Constitution (Article I, Section 8), the Congress has the sole power to declare war. If the Executive Branch deceives the Congress in this duty, it represents an attack of our democracy of the most serious nature. These Constitutional questions are not going away and must be answered forthrightly and completely by this Administration.

"I and 88 of my colleagues (that number is growing - more on that soon) asked the Administration to come clean about these troubling allegations. Our inquiries have been met with silence.

"The press has also been negligent in giving this matter the attention it deserves.

"I am committed to seeing this through until we get the answers we deserve. But I need your help.

"The conventional wisdom, which unfortunately governs Washington's political discourse, hold that the American people have long ago made peace with the mistakes or deceptions which led us into war. Help me prove them all wrong. I want to show the White House, the Press and my congressional colleagues that nothing could be further from the truth.
"

Thursday, May 26, 2005

Graduation and plagiarism

I just got back from walking in our graduation ceremony. I'm still not used to participating as a faculty member; it feels wrong to not be in the student row. But instead of walking across the stage, I got to sit there with my pretty colored hood on, look official, and chat with the local chemists about the various students we knew who were graduating.

While I still have an incredibly large stack of papers that need to be graded (I just gave my final exam today, and still have other papers to grade as well), instead of grading I've been spending most of my time writing academic dishonesty reports for the dean. So far I've found four five plagiarized papers; for each paper I have to confront the student, and then type up a multi-page report detailing both the plagiarism and the student's response. This is not the way I'd hoped to spend the evening, but given how the past few semesters have gone, I shouldn't be surprised.

[Update May 27, 7:30pm: Found another plagiarized paper today, and managed to get all the reports in to the dean. But my pile of grading is still far too high.]

Wednesday, May 25, 2005

A course on Linux

Linux Journal has an article on a Linux class being run by a couple of professors at Transylvania University. The article talks about how the professors planned the course (and ran a similar course last year), and includes a discussion of various textbooks, the goals of the course, the course outline, methods of assessment, and in-class activities the students will perform. As a side note, the course is being run with RedHat Fedora, not my currently installed flavor of Debian.

The class has been running through the month of May, and the article links to the class website (username guest1; password guest42), where you can currently access the course assignments, including this one:
"Introduction to Linux Administration
Lab 2 - chkconfig

Due Date: Wednesday, May 4th
Points : 25

1.Using chkconfig, determine which processes are currently active on your system.
2.For each service, write a small paragraph describing the purpose of the process.
3.Determine which processes you feel are necessary if you are going to use Linux as an ordinary desktop machine. Write a paragraph detailing why you do (or do not) decide that you need a certain process. In other words, give a good justification to your answer.
4.For the purpose of this assignment, do not concern yourself with the xinet.d srevices.
5.Your report must be written using Open Office. You will need to e-mail your report to me by noon on Wednesday.
6.You are to work with your lab partner. (I.e., the other person in your row.)

I might even do that assignment, even if I will be turning it in late.

Tuesday, May 24, 2005

Looking for that lost game manual?

Replacementdocs.com has more than 2000 scanned-in manuals for old (and new) computer games, all of them freely available. My SO's already found a number of NES manuals that we've been missing.

Via BoingBoing.

Bagram Collection Point followups

Here are a few more articles relating to the prison abuse at Bagram Collection Point in Afghanistan during 2002:
  • An AP article details the plea bargain of one of the soldiers (Specialist Cammack) described in the New York Times series. Specialist Cammack was the last soldier to beat a detainee, who died only a few minutes later (according to the New York Times); he received three months in prison.

  • The Star Tribune reports that there may be two different death certificates for one of the prisoners discussed in the New York Times articles.

  • CNN has two articles covering reactions to the New York Times articles. One discusses the UN's reaction, and the other covers president Karzai's reaction.

Monday, May 23, 2005

Morning reading

The New York Times has a two-article series detailing abuses that occurred at Bagram Collection Point, a US army prison in Afghanistan, during 2002. The two articles are:

In U.S. Report, Brutal Details of 2 Afghan Inmates' Deaths - May 20, 2005

Army Faltered in Investigating Detainee Abuse - May 22, 2005
"The story of Mr. Dilawar's brutal death at the Bagram Collection Point - and that of another detainee, Habibullah, who died there six days earlier in December 2002 - emerge from a nearly 2,000-page confidential file of the Army's criminal investigation into the case, a copy of which was obtained by The New York Times.

"Like a narrative counterpart to the digital images from Abu Ghraib, the Bagram file depicts young, poorly trained soldiers in repeated incidents of abuse. The harsh treatment, which has resulted in criminal charges against seven soldiers, went well beyond the two deaths
."
The articles are long and detailed, but here's a glimpse of what they contain:
"Mr. Dilawar was a frail man, standing only 5 feet 9 inches and weighing 122 pounds. But at Bagram, he was quickly labeled one of the 'noncompliant' ones.

"When one of the First Platoon M.P.'s, Specialist Corey E. Jones, was sent to Mr. Dilawar's cell to give him some water, he said the prisoner spit in his face and started kicking him. Specialist Jones responded, he said, with a couple of knee strikes to the leg of the shackled man.

"'He screamed out, "Allah! Allah! Allah!" and my first reaction was that he was crying out to his god,' Specialist Jones said to investigators. 'Everybody heard him cry out and thought it was funny.'

"Other Third Platoon M.P.'s later came by the detention center and stopped at the isolation cells to see for themselves, Specialist Jones said.

"It became a kind of running joke, and people kept showing up to give this detainee a common peroneal strike just to hear him scream out "Allah," ' he said. 'It went on over a 24-hour period, and I would think that it was over 100 strikes.'"

[snip]

"The findings of Mr. Dilawar's autopsy were succinct. He had had some coronary artery disease, the medical examiner reported, but what caused his heart to fail was 'blunt force injuries to the lower extremities.' Similar injuries contributed to Mr. Habibullah's [another prisoner's] death.

"One of the coroners later translated the assessment at a pre-trial hearing for Specialist Brand, saying the tissue in the young man's legs 'had basically been pulpified.'

"'I've seen similar injuries in an individual run over by a bus,' added Lt. Col. Elizabeth Rouse, the coroner, and a major at that time.
"
The articles provide even more details of the interrogations and deaths of the two inmates, and also describe the slow investigations that followed.

I'm back

My SO and I are back from our trip. Unfortunately, the coming week is finals week, so I'll be working frantically to make up for taking the weekend off.

Friday, May 20, 2005

A slug saves the trip

Yesterday we drove up to San Francisco to attend my mom's graduation. While the graduation ceremony went well, the rest of the trip hasn't been stellar.

First, as regular readers will remember, the two subs I lined up to cover my classes both ended up in the hospital over the weekend, forcing me to cancel my lecture and lab classes. Then our car started acting up on the drive north; the car made it to both the graduation and my parent's house, but not without causing much worrying and emitting worrying odors.

So, rather than sleeping late and relaxing on the couch today, we've been on the phone with mechanics who are trying to diagnose the frustratingly sporadic problems. It has been neither fun nor cheap.

However, while investigating who's been eating all the seeds from my dad's birdfeeder (our surprising discovery: birds!), we found this cute little slug climbing up the sliding glass door:


Slug on a piece of paper
How adorable!

Slugs are one of the few types of terrestrial mollusks; they're closely related to snails (but either lack a shell or have much reduced shells). My students often think, incorrectly, that slugs are just snails that have lost their shells. Slugs and snails are two completely different lineages; snails that lose their shells die, they do not turn into slugs.

The slug's head is at the lower right of the picture, and has two sets of tentacles. The smaller tentacles lower to the ground are the oral tentacles, which contain chemosensors, while the longer tentacles are cephalic tentacles, which contain photoreceptors. As the slug crawls over surfaces, it tastes the surface it's walking on by touching it at regular intervals with its oral tentacles.

There's no better way to brighten a day than to find a slug.

Thursday, May 19, 2005

New computer

My SO's new computer arrived a few days ago, and now our living room looks geekier than ever:

Geek central

From left to right in the picture above are Arashi (running Linux), Cecil, Nakago, and Samwise. [Quiz: who knows where each of these names came from?]

Samwise's monitor stand is indeed composed of old textbooks; O-chem has never been more useful. Nakago is the oldest Windows box, and will likely be shut down once we're done moving files, meaning that we'll be back to our usual three computers for two people.

And what's even cooler is how the setup looks at 2am with all the room lights turned off:

Computers at night
The view we woke up to this morning

Tangled Bank #28

Tangled Bank Blutton
Tangled Bank 28 has been posted over at Chronicles of a Medical Madhouse. I had planned to post this last night when I got home, but instead decided to take a short nap that ended up lasting until 2am ...

Tuesday, May 17, 2005

Tangled Bank Announcement

Tangled Bank Blutton
The next Tangled Bank will be hosted at Chronicles of a Medical Madhouse. Get your submissions in to MadhouseMadman@gmail.com by today at 6pm EST if you want to be included.

Monday, May 16, 2005

I'm hard on subs

I'm going to be attending my mom's graduation in the San Francisco area on Thursday, and thus have to miss classes on Thursday and Friday. This is the second-to-last week of classes, and my lab final exam is scheduled for Thursday and Friday, so I was careful to line up subs many weeks ago.

On Sunday I learned that one of my subs had just gotten out of the hospital, and had to cancel. And, just now, I learned that my other sub is currently in the hospital recovering from emergency surgery.

Lesson learned: Don't sub for me.

[Update: I wasn't able to find any other subs, so ended up having to cancel classes on Thursday and Friday and delay an exam. I've rarely seen my students so elated.]

Who says plants can't move fast?

Edwards et al. (2005) have a paper in Nature documenting an extremely speedy plant: the flowers of the bunchberry dogwood (Cornus canadensis) open in less than half a millisecond; as the flower explodes open, its stamens act like a trebuchet, flinging pollen into the air.

Nature's website has a few snazzy slow-motion videos (10,000 fps) of the flower opening in its supplementary information section (free), along with two of the paper's figures (also free).

Edwards J, D Whitaker, S Klionsky, and MJ Laskowski. 2005. Botany: A record-breaking pollen catapult. Nature 435 164 | doi: 10.1038/435164a

Via BoingBoing.

Sunday, May 15, 2005

Tangy black-eyed pea, kielbasa, and greens soup

I came home on Wednesday to find my SO cooking a soup filled with onions, garlic, black-eyed peas, sausage, and greens. I ate the soup for dinner that night, for lunch the next day, and then again for breakfast the day after that. In short, I loved it, so it's this week's end-of-the-week recipe blogging post. Unlike many of my recent recipe postings, this recipe was created entirely by my SO.

In addition to being hearty and flavorful, this soup is also quite good for you. Thanks to a full pound of turnip greens, another pound of black-eyed peas, and other assorted vegetables, the soup contains 10g of fiber (40% of the daily requirement for a 2000-calorie diet), 286% of the RDA for vitamin A, 86% of the RDA for vitamin C, 23% of the RDA for calcium, and 36% of the RDA for iron, per serving, assuming 8 large servings. Approximately 39% of the soup's 450 calories come from fat, 42% from carbohydrates, and 20% from protein; it contains 20g of fat (6.3g saturated) per serving, which is just about 30% of a 2000-calorie diet's daily fat and saturated fat (values calculated by MasterCook).

2 tablespoons olive oil
1 pound kielbasa, halved and sliced into ~1/2" thick pieces
5 medium carrots, peeled and sliced ~1/8 to 1/4" thick
4 medium onions, finely chopped
8 cloves (~1/2 bulb) garlic, minced or pressed with a garlic press
1 pound dried black-eyed peas, rinsed and sorted (to remove any bad peas)
Water to cover the peas
1 pound turnip greens (we used frozen)
Salt to taste (we think we used ~2 teaspoons)
Pepper to taste (we think we used ~1/2 teaspoon)
~3 whole limes

1. In a large, nonstick, heavy-bottomed pot, heat the oil over medium-high heat.
2. When the oil is hot, add the kielbasa and fry, stirring, until the sausage begins to brown (~5-10 minutes).
3. Add the onions and carrots, and cook, stirring often, until they begin to soften (~5-10 minutes). My SO chopped the onions and sliced the carrots using our food processor.
4. Add the garlic, and continue to cook, stirring, for another few minutes (~3 minutes).
5. Add the black-eyed peas to the pot along with enough water to cover them by a couple of inches. If you want a thicker soup, add less water; if you want a thinner soup, add more water.
6. Simmer, covered, until the black-eyed peas are tender, approximately an hour and a half. Stir occasionally, and add more water if the soup is looking too thick.
7. Once the peas are tender, add the greens, salt, and pepper (vary the amounts of salt and pepper to your taste). Return to a simmer, and cook for another 10 minutes, or until the greens are cooked through.
8. Ladle into bowls, and serve with fresh lime juice to taste (we used a couple of teaspoons per bowl).

Fresh-squeezed lime juice is an essential part of the recipe; its tanginess brightens the flavors of the soup. Lemons make an OK substitution, though if you were really in a pinch, you could probably substitute vinegar.

Substituting mustard greens or collard greens for turnip greens should work well; spinach could probably work too, but it might just fall apart while cooking.

Feel free to vary the recipe to fit your preferences. Some easy variations we've thought of include:
  • Reduce the garlic, if you're not as addicted to it as we are.
  • Mash some of the soup with a potato masher, if you want it creamier.
  • Reduce the sausage, or use low-fat sausage, if you want a lower-fat soup.
  • If you wanted the sausage to retain more of its flavor, you could fry it first, then remove it from the pot while cooking the rest of the soup, finally adding it back to the pot with the greens.

Saturday, May 14, 2005

Schwarzenegger continues breaking promises

Governor Schwarzenegger just released a revision to his state budget proposal yesterday, and there was some good news: the state will be getting $3.9 billion more in revenue than was expected back in January. The LA Times has a detailed story on the changes to the budget.

Seeing as the governor reneged on his promise to fully fund education, shorting programs by $2 billion in his January budget, this windfall would have been the perfect opportunity for Schwarzenegger to keep his promise. It seems as though he could have fully funded education to levels required by proposition 98, and still had money left over for other programs.

But no, from what I can tell the education budget is being increased by only around $250 million (earmarked specifically for class size reduction in specific grades), which amounts to only about 10% of the amount by which Schwarzenegger shortchanged education in January.

Friday, May 13, 2005

Antibiotic resistance in bacteria

As soon as antibiotics are applied to a population of bacteria, only those bacteria that have the ability to survive in the presence of the antibiotic reproduce, thus resulting in strong selection for bacteria with antibiotic resistance. If the bacteria don't already have genes for antibiotic resistance, they generally have to rely on random mutations, or genetic transfers from other bacteria that already have these genes, to acquire antibiotic resistance.

However, a recent journal article (Cirz et al. 2005; my dad just sent me the synopsis), reports on a mechanism some bacteria use to increase their mutation rate in response to certain antibiotic drugs, thus causing faster evolution of resistance to those drugs. The article is in PLoS Biology, an open-access journal, so the full text of the paper is freely available. It's a good read.

Antibiotics known as quinolones (e.g., Ciprofloxacin, aka Cipro) interfere with the normal functioning of topoisomerases (proteins that help maintain DNA structure) in bacteria; this interference causes DNA damage, and eventually bacterial cell death. Bacteria can evolve resistance to these drugs, and the required mutations to obtain resistance are known:
"Resistance to ciprofloxacin requires mutations in the genes that encode the topoisomerases (gyrA and gyrB, encoding gyrase, and parC and parE, encoding topoisomerase IV) or in the genes that affect cell permeability or drug export"
By altering the function of the topoisomerases, the quinolones also stop the repression (by LexA) of a set of genes known as SOS genes. These (normally repressed) genes include three DNA polymerases (proteins that synthesize / repair DNA) that often mutate DNA as they work on it; these DNA polymerases are not essential for bacterial survival, as bacteria have other DNA polymerases they use for typical DNA replication. The end result of all this molecular biology is that bacteria treated with quinolones should begin producing DNA polymerases that cause mutations in the bacteria's own DNA; Cirz et al. set out to verify this experimentally.

Cirz et al. first infected mice with pathogenic strains of E. coli, and then administered ciprofloxacin; after 72 hours they found that approximately 3% of the E. coli in the mice had become resistant to the antibiotic (figure 1, filled circles). However, when they infected mice with a strain of E. coli that could not de-repress the SOS genes (by preventing autoproteolysis of LexA), they found that none of the bacteria in the mice evolved resistance to ciprofloxacin after 72 hours (figure 1, filled triangles).

Cirz et al. then compared the mutation rates of E. coli before and after ciprofloxacin treatment, and found that exposure to ciprofloxacin increased the mutation rate by approximately 10^4 (from 9.0 × 10−10 mutants/viable cell/d to 1.8 × 10−5 mutants/viable cell/d). However, when they examined a strain of E. coli that could not de-repress the SOS genes, they found that mutation rates after exposure to ciprofloxacin were 100-fold lower than those of standard E. coli exosed to ciprofloxacin.

In summary, Cirz et al. found that administration of quinolones to bacteria increased bacterial mutation rates, and thus promoted the evolution of resistance to the antibiotics. Or, as the paper's authors say,
"the mutations that confer resistance to ciprofloxacin and rifampicin are not simply the result of unavoidable errors accumulated during genome replication, but rather are induced via the derepression of genes whose protein products act to significantly increase mutation rates."
Then the paper's authors go on to suggest how this knowledge can be used to help prevent, or at least reduce, the evolution of antibiotic resistance:
"The traditional paradigms of DNA replication and mutation suggest that resistance-conferring mutations are the inevitable consequence of polymerase errors, and offer no obvious means for intervention. In stark contrast, the model described above suggests that bacteria play an active role in the mutation of their own genomes by inducing the production of proteins that facilitate mutation, including Pol IV and Pol V, as has been suggested with other forms of mutation. In turn, this suggests that inhibition of these proteins, or the prevention of their derepression by inhibition of LexA cleavage, with suitably designed drugs, might represent a fundamentally new approach to combating the emerging threat of antibiotic-resistant bacteria."

Reference:

Cirz RT, JK Chin, DR Andes, V de Crécy-Lagard, WA Craig, FE Romesberg. 2005. Inhibition of Mutation and Combating the Evolution of Antibiotic Resistance. Public Library of Science Biology 3: e176. Full-text HTML, PDF.

Thursday, May 12, 2005

EPA lead rules

The LA Times reports that the EPA is not going to implement mandated safety regulations for lead-based paints in homes, and is instead looking into voluntary suggestions for safe handling of the materials.
"The regulations were to require that only certified contractors, using workers trained in lead-safety practices, be used for remodeling work in buildings constructed before 1978, when the use of lead-based paint for housing was banned.

[snip]

"EPA officials emphasize that they are concerned about lead exposure and its effect on children. They also point to an internal study showing that the cost of the regulations — $1.7 billion to $3.1 billion annually — could be an overwhelming burden for the mostly small businesses that renovate buildings.

"However, an agency estimate showed that such rules would provide health benefits of greater value, from $2.7 billion to $4.2 billion annually.

[snip]

"Under a 1992 amendment to the Toxic Substances Control Act, regulations governing building renovations and lead safety were to be in place by 1996, but the EPA fell behind schedule. In 2003, the agency issued a report saying it expected to finish the rules by 2005.
"

Wednesday, May 11, 2005

Congress asks Bush about war planning

A recently leaked memo from the UK appears to confirm that the Bush administration was set on a course of war with Iraq back in the summer of 2002, and even implies that the administration was "fixing" intelligence facts. Representative John Conyers has blogged about this memo, both on his own blog and on DailyKos. He's also linked to the letter (full-text PDF) that 88 Congress members sent to Bush regarding the memo.

Here's the letter in full, as it explains the circumstances better than I can:

Dear Mr. President:

We write because of troubling revelations in the Sunday London Times apparently confirming that the United States and Great Britain had secretly agreed to attack Iraq in the summer of 2002, well before the invasion and before you even sought Congressional authority to engage in military action. While various individuals have asserted this to be the case before, including Paul O’'Neill, former U.S. Treasury Secretary, and Richard Clarke, a former National Security Council official, they have been previously dismissed by your Administration. However, when this story was divulged last weekend, Prime Minister Blair'’s representative claimed the document contained "“nothing new."” If the disclosure is accurate, it raises troubling new questions regarding the legal justifications for the war as well as the integrity of your own Administration.

The Sunday Times obtained a leaked document with the minutes of a secret meeting from highly placed sources inside the British Government.(1) Among other things, the document revealed:
  • Prime Minister Tony Blair chaired a July 2002 meeting, at which he discussed military options, having already committed himself to supporting President Bush'’s plans for invading Iraq.

  • British Foreign Secretary Jack Straw acknowledged that the case for war was “"thin"” as “Saddam "was not threatening his neighbours and his WMD capability was less than that of Libya, North Korea, or Iran."

  • A separate secret briefing for the meeting said that Britain and America had to "“create"” conditions to justify a war.(2)

  • A British official “"reported on his recent talks in Washington. There was a perceptible shift in attitude. Military action was now seen as inevitable. Bush wanted to remove Saddam, through military action, justified by the conjunction of terrorism and WMD. But the intelligence and facts were being fixed around the policy.”"
As a result of this recent disclosure, we would like to know the following:
  1. Do you or anyone in your Administration dispute the accuracy of the leaked document?

  2. Were arrangements being made, including the recruitment of allies, before you sought Congressional authorization go to war. Did you or anyone in your Administration obtain Britain'’s commitment to invade prior to this time?

  3. Was there an effort to create an ultimatum about weapons inspectors in order to help with the justification for the war as the minutes indicate?

  4. At what point in time did you and Prime Minister Blair first agree it was necessary to invade Iraq?

  5. Was there a coordinated effort with the U.S. intelligence community and/or British officials to "“fix"” the intelligence and facts around the policy as the leaked document states?
We have of course known for some time that subsequent to the invasion there have been a variety of reasons proffered to justify the invasion, particularly since the time it became evident that weapons of mass destruction would not be found. This leaked document - essentially acknowledged by the Blair government - is the first confirmation that the rationales were shifting well before the invasion as well.

Given the importance of this matter, we would ask that you respond to this inquiry as promptly as possible. Thank you.

(1) See Attached Document, “Secret and strictly personal - UK eyes only,” July 23, 2002.

(2) See Michael Smith, “Blair Hit By New Leak of Secret War Plan, ” The Sunday Times-Britain, May 1, 2005.

Ever wonder why the terrorist alert levels were raised?

According to Tom Ridge in this USA Today article, the terrorist alert levels weren't being raised because the Department of Homeland Security was concerned:
"The Bush administration periodically put the USA on high alert for terrorist attacks even though then-Homeland Security chief Tom Ridge argued there was only flimsy evidence to justify raising the threat level, Ridge now says.

"Ridge, who resigned Feb. 1, said Tuesday that he often disagreed with administration officials who wanted to elevate the threat level to orange, or 'high' risk of terrorist attack, but was overruled."

[snip]

"'More often than not we were the least inclined to raise it,' Ridge told reporters. 'Sometimes we disagreed with the intelligence assessment. Sometimes we thought even if the intelligence was good, you don't necessarily put the country on (alert). ... There were times when some people were really aggressive about raising it, and we said, 'For that?' '
"

Tuesday, May 10, 2005

The Orange Man

Back in April (yes, I'm behind on my reading), Orac wrote an excellent post titled The Orange Man; it's a great example of why "alternative medicine that is ineffective is not harmless."

If you're at all interested in an alternative treatment for just about any possibly lethal condition, read this post first.

Monday, May 09, 2005

Iraq picture

Michael Yon, a photographer/blogger who is currently in Iraq, recently posted a photograph of an American soldier cradling a wounded little girl. It's a powerful image that has been getting a lot of media attention. Via BoingBoing.

Saturday, May 07, 2005

Lemon butter frosting

We're spending this weekend helping a friend paint a few rooms in his new house. We just got the first coat up today, and will be spending tomorrow putting up the second coat. We baked a cake last night, and gave it to our friend today as a mini-housewarming gift; we frosted the cake with our favorite lemon butter frosting, and thus the frosting is this week's end-of-the-week recipe blogging post.

This frosting is extremely simple to make; it can be whipped up in less than 15 minutes, and only requires butter, powdered sugar, lemons, and a bit of salt. The finished frosting is very sweet, with a strong lemon flavor; it's a good compliment to many cakes, and we use it regularly on our lemon cakes. This frosting makes enough to coat a 9"x13" sheet cake generously.

1 teaspoon lemon zest
6 tablespoons butter
1/4 teaspoon salt
3 cups powdered sugar, sifted
1/4 cup lemon juice, freshly squeezed

1. Put the lemon zest, butter, and salt into a mixing bowl, and beat until smooth. We use our KitchenAid stand mixer for this, though you could also do it by hand if the butter were softened ahead of time.
2. Add approximately 1/4 of the powdered sugar to the butter, and beat until it is incorporated. Then add approximately 1/4 of the lemon juice, and beat until it is incorporated.
2. Continue alternately adding the powdered sugar and lemon juice until they are all mixed in. We find that using 1/4 cup lemon juice gives a good texture, but you can vary the amount of lemon juice to make a thicker or thinner frosting.
3. Frost your cake.

Frosting a cake is an art, but luckily the frosted cake doesn't have to look pretty to taste good. One trick is to apply a very thin coating of frosting (a "crumb coat") before putting the rest of the frosting on the cake; this crumb coat helps prevent the frosting from picking up little bits of the cake as you spread the final layer. I like to slide the edge of a serrated knife over the top of a frosted cake as a decorative touch.

We found a version of this recipe online many, many years ago, and have long since lost the original link.

Friday, May 06, 2005

An invertebrate iPod

Dope on the Slope has a review of the original iPod; they're almost as cute as my much-beloved Manduca. Via Pharyngula.

Say goodbye to roadless areas

The Clinton-era ban preventing road construction in large areas of national forests ("roadless areas") has been removed by the Bush administration, and replaced with a rule that allows state governors to petition for changes to the management policy of previously roadless areas (to allow road construction, for instance). The full text of the rule change, along with rather unsatisfactory responses to public comments, is available here.

There are news articles on this topic just about everywhere, including CNN, the LA Times, and the NY Times. Environmental groups are, understandably, unhappy; read more at the Sierra Club, the National Resources Defence Council, and the National Audubon Society.

To read about another Bush administration change to UDSA forestry rules, see this earlier post.

Thursday, May 05, 2005

Want your weather info for free?

The EFF has a short alert, Protect Public Weather Data, urging readers to send a letter to their senators to protest a bill that would prevent the National Weather Service from continuing to release user-friendly weather information. The NWS website is a great source for weather information, including local forecasts (enter your zip in the box on the left), detailed satellite imagery, and even ozone concentration maps for some states. Most of their maps have the ability to show looping views of the last 24 hours, which can be quite interesting (e.g., the GOES visual satellite loop).

Via BoingBoing.

Tuesday, May 03, 2005

Monday, May 02, 2005

Spore - a biological perspective

[Note: The following post is based on information obtained from one GameSpy article, and is intended to be a discussion of the biology relevant to Spore; this is not a review of the game.]

The Game

Back in March, Penny Arcade linked to a GameSpy article summarizing a talk by Will Wright on his newest game, Spore. The game is still in development, but it's based on an intriguing idea: instead of using premade artwork and animations to populate the game's visual realm (as in The Sims), Wright wants to have the software dynamically create all the animations, characters, and structures in the game, based on each player's input.

The premise behind Spore, as it has been described, is that each player starts out controlling a single-celled organism, probably a protist of some sort, that the player can then "evolve" into more complex organisms. The ability to "evolve" an organism occurs only after the player has helped their organism survive enough challenges (e.g., consuming enough food), and "evolution" occurs by the player choosing between specified morphological characteristics that can be added to each organism. After lots of "evolution," the player ends up with a fully 3-D, multicellular creature (an animal), which continues to "evolve" through the addition of even more structures. After the creatures have "evolved" to live on land, the creatures can "evolve" culturally, including building societies, which can "evolve" the ability to travel to and colonize new worlds, all the while interacting with organisms created by other players.

The article professes that the game editor is extremely flexible, and can build just about any organism:
"Sure enough, just about anything was possible with the editor: Wright demonstrated an upright dog whose front legs were twice as long as his back legs, a creature with an enormous floppy eggplant-shaped head that had no less than a dozen hungry beaks, a six-legged critter with two snapping heads that skittered along very fast, and finally a fully-functional Care Bear. (!)

"Regardless of what you could dream up, the game would find a way to make it work. Top-heavy characters would bobble along awkwardly, creatures with branching networks of a dozen legs would learn to walk, and animations for fighting and eating would be generated on the fly."
While the technology behind the game sounds fascinating, based on the review it appears that the game has clear biological limitations, and even a few inaccuracies. This post looks at the game from a biological perspective, and examines what the game could be like if it were more biologically realistic.

"Evolution"

The first, and probably largest, biological problem is that evolution appears to occur solely by the player adding specified characteristics to their organisms. This is not how biological evolution works.

Evolution (by natural selection) occurs through selective pressures differentially changing the fitness of organisms with different character states; those organisms with the characteristics that confer the highest fitness in their current environment survive, reproduce, and pass their genes on to the next generation at higher frequencies than other organisms, so their genes become more prevalent in the population. While I understand the reasoning behind forcing the player to choose from a specific set of characteristics, it would be more biologically accurate if the player-controlled organisms had variation appear in their characteristics as they reproduced, which the player would then have to exploit to encourage their organisms to evolve in a specific direction. Non-player organisms could function in the same manner, and thus the ecosystem of the game world would be constantly evolving and presenting new challenges to the player. The game could even have characteristics determined by mutable genes (which could be hidden from the player), adding an even more realistic touch.

Biological diversity

It sounds as though the game is entirely focused on chemoorganotrophs (organisms that obtain their energy from reduced organic molecules, e.g., other organisms), and completely ignores phototrophs (organisms that get their energy from light) and chemolithotrophs (organisms that get their energy from reduced inorganic molecules, e.g., ferrous iron or sulfates). By removing both of these types of organisms, Wright removes two critical elements of functioning ecosystems. From a gameplay perspective, directing the evolution of phototrophs would pose its own unique challenges, such as attempting to develop defenses against the herbivores of the world, and if chemolithotrophs were allowed, players could evolve an organism that lived on the technological products of other organisms in the game world.

The review mentions that players can attempt to invade worlds inhabited by other players' organisms, and this appears to occur primarily by animal-based fighting. What if, instead of fighting with lasers and spaceships, players could evolve an invasive species of inedible plants and colonize the enemy planet with it, out-competing the planet's native plants and starving the enemy organisms of their food? Or, what if players could evolve some chemolitotrophic bacteria that would feed on the technological structures created by the enemy race, and thus reduce the enemy race's spaceships and machine guns to piles of rubble before the invading forces ever set foot on the planet? Or, even better, what if a player's primary organism was the chemolithotrophic bacteria, and they attempted to spread through the universe by feeding on other players' technology?

The game completely ignores non-animal chemoorganotrophic organisms like fungi, which still get energy from digesting other organisms, yet which grow and survive in a completely different manner (their bodies are composed of long, filamentous strands that grow through whatever structure they're living in). There are even some predatory fungi (that set traps for nematode worms), so it could be neat, and biologically realistic, to present players with the option to evolve into predatory fungi, which might even include the ability to feed on other player-created organisms in the world.

The game also seems to completely ignore parasites, which are some of the most interesting animals around. Allowing players to evolve creatures into parasites would drastically increase the number of possible interactions available in the game world. Going back to my interstellar colonization example, instead of sending down an army to invade a planet, a player could "evolve" a few species of parasites that could either weaken or kill the enemy species, or possibly even take control of them (e.g., Stargate's Goa'uld).

Vertebrates, vertebrates, vertebrates ...

The game directs players not just toward animals, but toward vertebrate animals. GameSpy lists a few of the possible evolutionary characteristics:
"Wright could give his creature extra vertebrae, he could give it fins or tails to move faster, he could add claws or extra mouths."

"More importantly, you could add functional elements, like heads, mouths, eyes, tails, fins, claws, even legs and feet."
Notably absent from this list are characteristics found primarily in invertebrate animals, such as tracheae, tentacles, shells, exoskeletons, jet propulsion systems, various invertebrate mouthparts (e.g., piercing tubes, muscular pharynxes), and antennae.

The animals described in the article are all vertebrate animals; however, vertebrate animals are not the most successful animals on Earth. In both number of named species and current population levels, arthropods, with their exoskeletons and jointed appendages, are the animal rulers of the planet (though bacteria outstrip any animal in population levels), and arthropods are arguably the best adapted organisms to terrestrial life. It's distressing that players might be prevented from evolving their organisms into one of the most successful lineages on the planet.

Ecology, ethology, and spaceflight

The game also seems to link specific morphological characteristics to ecological niche changes:
"Wright proceeded to add not two, but three legs to his creature. Then he let it loose. Now, suddenly, his creature could walk. And he did so -- he walked right out of the sea and onto the land."
As a minor note, this quote implies that two legs are the default for living on land; this is not the case. 99+% of terrestrial animal species with limbs walk on all four, six, eight, or more, of them, and even humans have four limbs. There are no completely terrestrial organisms extant (that I can think of) that have only two limbs.

More importantly, this quote seems to imply that legs are a prerequisite for terrestriality; they are not. Terrestrial mollusks (snails and slugs) and annelids (worms) do just fine without any limbs, and thus it would be fascinating to give players multiple options through which they could become terrestrial. Terrestrial mollusk bodies are highly mutable and expandable, and one can imagine that if mollusks were given the right "evolutionary" pushes, players could develop a wide array of functional terrestrial body plans. Also, there are many aquatic organisms that have legs (e.g. crustaceans), so organisms that evolve legs shouldn't necessarily switch to living on land. Why not allow civilizations of organisms to evolve in the oceans?

Once players have evolved a terrestrial creature, the game appears to take a very human-focused viewpoint, implying that evolving sentience and sociality is the ultimate step in evolution (since without it you can't advance to the games next stages):
"We thought Wright had made his point but were surprised when he went back into the game and showed us how it was about to take a weird turn. See, along with adding extra legs and mouths and tails and claws to your creature, you could also slowly invest in the creature's brain power. When you maxed out the creature's brain, it suddenly developed ... sentience!

"And here, the game shifted focus. Instead of managing a single creature, you were suddenly in charge of a whole tribe of your creatures. Wright's odd three-legged little critters danced around a hut in the center of a village. You could still evolve your creatures, but now, instead of buying new appendages or physical features, you bought them things like fire or weapons. Wright built a fire pit and his critters danced around it (making up a three-legged dance as they went along.) He built a drum and they started playing with it."
While evolving sociality has certainly helped a few specific lineages become more successful (e.g., Hymenoptera [bees, ants, and wasps], Isoptera [termites], Mammalia), the vast majority of organisms on Earth are highly successful with neither complex social behaviors nor high intelligence. Thus, if you have a game that lets players design whatever organism they want, there should be no preference given to organisms that have intelligence or social behavior.

If the game designers wanted players to be able to travel in space and colonize new worlds (so they could advance to the next game stages), why not present players with the option of "evolving" characteristics that would allow survival in space without technology? One could imagine space-faring dragonflies (ala Lexx), hymenopterans (ala Starcraft), or any other number of fantastic creatures, all of which would significantly increase the strategic components involved in interspecific relations (e.g., how does a dragonfly communicate with, or fight, a race of large mammals?)

A wrapup

Wright has used a grounding in reality to create some of his earlier successes; one of the reasons I enjoyed playing The Sims was because it was based on research investigating how humans actually spend their time, not how humans want to spend their time. If Wright were to provide players with a game strongly grounded in biological theory, and allowed players to evolve organisms with the true range of biological diversity, the game would have a tremendous array of possible trajectories for players to follow. All of these trajectories could be successful in their own way, making the game much more enjoyable and replayable.