I'll be on the road for the next few weeks, as my SO and I travel to Canada so I can teach my field course. This trip will be shorter than our trips of the past few years, though we'll still drop by Victoria for a few days to enjoy another round of Big Muckle Giant Tea for Two and some Haultain's fish and chips (hopefully they won't be closed this year).
I have no idea how much time I'll have to post, or even if I'll have net access, so posting will likely be intermittent until mid-June.
Wednesday, May 31, 2006
Ubuntu's newest release
Ubuntu's newest release (6.06 LTS) will be released on June 1; unfortunately, I'll be on the road then, so won't be able to download it until I get back in a few weeks. This release is a landmark for Ubuntu, as it is planned to be supported for five years, even though newer releases are going to be released at six-month intervals.
Ubuntu is a popular1 Linux distribution that is intended to be extremely easy for novices to use. Ubuntu is based on Debian (the Linux distribution I currently use), and since my trial run of Ubuntu back in March was mostly problem free, I'm extremely tempted to switch. Ubuntu has a LiveCD that you can download (from here), burn to a CD, and then try out on your computer without actually installing anything onto your computer (I've written more about that here). If you've been wanting to see what using Linux is like, Ubuntu's LiveCD is a great way to do it.
1 - Ubuntu was ranked 1st in the "Favorite Distribution" category of Linux Journal's 2005 Readers' Choice Awards.
Ubuntu is a popular1 Linux distribution that is intended to be extremely easy for novices to use. Ubuntu is based on Debian (the Linux distribution I currently use), and since my trial run of Ubuntu back in March was mostly problem free, I'm extremely tempted to switch. Ubuntu has a LiveCD that you can download (from here), burn to a CD, and then try out on your computer without actually installing anything onto your computer (I've written more about that here). If you've been wanting to see what using Linux is like, Ubuntu's LiveCD is a great way to do it.
1 - Ubuntu was ranked 1st in the "Favorite Distribution" category of Linux Journal's 2005 Readers' Choice Awards.
Tuesday, May 30, 2006
Deducing adjunct salaries
Last week I got an e-mail from a regular reader (thanks Endora!) who asked a seemingly simple question (slightly edited to anonymize it):
Bakersfield College is one of three colleges in the Kern Community College District, and as with many colleges, the district website is often the best place to look for information on faculty contracts, pay schedules, and other human resources information. Unfortunately, the district website doesn't have a handy little "How much will I get paid if I'm an adjunct instructor" page. Instead, I had to read through three documents on their website to figure out the pay rate:
Thus we see the reality of adjunct salaries: adjuncts must have a master's degree to even quality for the job, yet get paid less than $15,000 per year (assuming they teach a full adjunct load for two semesters a year). This is why adjuncts often become "freeway fliers" - they must travel from district to district (note that the limitation on LHEs is a district limit, not a college limit) in order make enough to pay the rent.
For comparison, the full-time faculty salary schedule of the Kern district is clearly posted (PDF), and a minimally qualified and minimally experienced full-time instructor in the Kern district gets paid $45,920 per year (two semesters); the vast majority of full-time faculty earn well over $50,000 per year. We can now hypothesize why it's so difficult to find adjunct faculty pay rates on college websites: the administrators are (or at least should be) embarrassed by how low the pay is.
Of course, if you're an adjunct trying to figure out how much you'd get paid, you probably don't want to go digging through the negotiated contracts of each community college district you're pondering working in. Thus, an easier way to figure this out is to contact someone at the college; I'd suggest e-mailing either someone in the human resources department, or the department chair of the department you may be teaching in.
In fact, if you'd like to start adjunct teaching somewhere, the best way to start is to e-mail a CV to the department chair of the department you want to work in. While you may not get a reply (and thus you should e-mail the chairs of many departments), the chair will probably put your CV in a file so they can call you when they're scheduling classes, or when an instructor backs out at the last minute (at which time they'll give you the classic "Can you teach a class that starts tomorrow at 7:30am for me?" call).
And, if you're an adjunct looking for that elusive full-time faculty position, you might be interested in a series of posts I wrote on applying for a full-time community college job (links to all the posts can be found here).
If any other readers have questions, please feel free to e-mail me. I'd be happy to start up a little "Radagast Responds" series.
I'm an adjunct instructor at a 4-year university in the southeastern US and an adjunct instructor at a 2 year community college. Since we might be moving to Bakersfield, California, I need to start looking around. Do you know a website I can look at to see the payscale for adjunct faculty?While community college pay scales are almost always public information, that information is rarely easy to obtain. For instance, if you go to Bakersfield College's website in search of pay scales for adjunct faculty, you'll finds lots of information about when timecards are due, and might even find that they're looking for adjunct faculty (on this page), but I couldn't find anything on how much adjunct instructors are actually paid.
Bakersfield College is one of three colleges in the Kern Community College District, and as with many colleges, the district website is often the best place to look for information on faculty contracts, pay schedules, and other human resources information. Unfortunately, the district website doesn't have a handy little "How much will I get paid if I'm an adjunct instructor" page. Instead, I had to read through three documents on their website to figure out the pay rate:
- Adjunct faculty salary schedule (PDF) - This document sounds like it should have all the information we need in it. The document does indeed provide information on pay rates: they pay $787.50 per weekly faculty contact hour (WFCH). Unfortunately, they don't specify what a WFCH is, how many WFCH's there are per course, or how many WFCH's an adjunct can teach.
- Adjunct faculty contract (PDF) - When in doubt, read the contract. This document does indeed have lots of details on adjunct faculty loads, including the limitation that adjunct loads are limited to 60% of what full-time loads are. This, of course, begs the question of what a full-time faculty load is. The adjunct faculty contract does not answer that question.
- Full-time faculty contract (PDF) - This has a whole lot of not terribly useful (for adjuncts) information, but the contract does specify that normal faculty loads are 15 LHE per semester. A LHE is approximately equivalent to one unit (or hour) of lecture, though labs often (but not always; it depends on the district) count for less (e.g., 1 hour of lab often gets paid as less than 1 LHE).
Thus we see the reality of adjunct salaries: adjuncts must have a master's degree to even quality for the job, yet get paid less than $15,000 per year (assuming they teach a full adjunct load for two semesters a year). This is why adjuncts often become "freeway fliers" - they must travel from district to district (note that the limitation on LHEs is a district limit, not a college limit) in order make enough to pay the rent.
For comparison, the full-time faculty salary schedule of the Kern district is clearly posted (PDF), and a minimally qualified and minimally experienced full-time instructor in the Kern district gets paid $45,920 per year (two semesters); the vast majority of full-time faculty earn well over $50,000 per year. We can now hypothesize why it's so difficult to find adjunct faculty pay rates on college websites: the administrators are (or at least should be) embarrassed by how low the pay is.
Of course, if you're an adjunct trying to figure out how much you'd get paid, you probably don't want to go digging through the negotiated contracts of each community college district you're pondering working in. Thus, an easier way to figure this out is to contact someone at the college; I'd suggest e-mailing either someone in the human resources department, or the department chair of the department you may be teaching in.
In fact, if you'd like to start adjunct teaching somewhere, the best way to start is to e-mail a CV to the department chair of the department you want to work in. While you may not get a reply (and thus you should e-mail the chairs of many departments), the chair will probably put your CV in a file so they can call you when they're scheduling classes, or when an instructor backs out at the last minute (at which time they'll give you the classic "Can you teach a class that starts tomorrow at 7:30am for me?" call).
And, if you're an adjunct looking for that elusive full-time faculty position, you might be interested in a series of posts I wrote on applying for a full-time community college job (links to all the posts can be found here).
If any other readers have questions, please feel free to e-mail me. I'd be happy to start up a little "Radagast Responds" series.
Monday, May 29, 2006
Updates
I've left a few threads hanging over the course of the semester, and want to wrap them up before too much time passes. So, without further ado:
- I haven't heard a word about the NSF grant I submitted, and don't expect to until September.
- Due to administrative policies that I do not comprehend, my online course proposal was tabled by a committee until September. Assuming the proposal is approved in September, I should still be able to teach it in fall 2007 (as was originally planned).
- Back in March I was excited by a proposal that, if funded, might have allowed me to dedicate a large chunk of time to some research projects I've been trying to get started. The proposal was funded, but for less than 50% of what we'd requested, removing the possibility of release time for research. So, I won't be doing any field research this coming fall.
- The administration also made it clear that they would not give me any release time if I was to continue as department chair in the fall; while I enjoyed certain aspects of the position, I decided a few months ago that I wasn't going to do the job unless I was given the release time to do it right. Thus, I am no longer department chair.
- These caterpillars have still not eclosed; the lazy buggers are just sitting as pupae in a cage in my lab.
- I've definitely found a new hobby in playing German-style board games.
- Our bathroom remodel is still in progress, though (thanks to the work of a concrete contractor) our bathroom floor has now been leveled and prepared for tiling. One of our primary goals this summer is to get at least one (and hopefully two) of our bathrooms finished. (yes, you can laugh uproariously now)
- The replacement of our backyard fence was successfully completed (and the block wall has been standing for a few months now). Yes, that's right ... we actually completed a remodeling project (thanks largely to hiring qualified people and doing none of the work ourselves).
Sunday, May 28, 2006
Political news of the week take 14
[See also: political news of the week takes 13, 12, 11, 10, 9b, 9a, 8, 7, 6, 5, 4, 3, 2, and 1.]
Due to being busy for the past two weeks, I skipped last week's news post. Here are this week's articles:
The Debate Over Immigration Reform - An excellent piece by the New York Times that compares the recent immigration bills passed by the Senate and House.
Due to being busy for the past two weeks, I skipped last week's news post. Here are this week's articles:
The Debate Over Immigration Reform - An excellent piece by the New York Times that compares the recent immigration bills passed by the Senate and House.
A showdown is looming over the most substantial overhaul of immigration law in 20 years. The Senate has passed a bill that would toughen border security and put most illegal immigrants on a path to citizenship. In contrast, the House has passed legislation that offers no provision for citizenship. President Bush is also deeply involved in the immigration debate and generally favors the provisions present in the Senate bill. The next step is for Senate and House leaders to meet in conference to try to reconcile their separate bills. The gulf between the two versions is so vast, and the politics of immigration so heated in this election year, that the prospects for a deal remain murky at best.Misjudgments Marred U.S. Plans for Iraqi Police
As chaos swept Iraq after the American invasion in 2003, the Pentagon began its effort to rebuild the Iraqi police with a mere dozen advisers. Overmatched from the start, one was sent to train a 4,000-officer unit to guard power plants and other utilities. A second to advise 500 commanders in Baghdad. Another to organize a border patrol for the entire country.Lawmaker: Marines killed Iraqis ‘in cold blood’:
Three years later, the police are a battered and dysfunctional force that has helped bring Iraq to the brink of civil war. Police units stand accused of operating death squads for powerful political groups or simple profit. Citizens, deeply distrustful of the force, are setting up their own neighborhood security squads. Killings of police officers are rampant, with at least 547 slain this year, roughly as many as Iraqi and American soldiers combined, records show.
...
Like so much that has defined the course of the war, the realities on the ground in Iraq did not match the planning in Washington. An examination of the American effort to train a police force in Iraq, drawn from interviews with several dozen American and Iraqi officials, internal police reports and visits to Iraqi police stations and training camps, reveals a cascading series of misjudgments by White House and Pentagon officials, who repeatedly underestimated the role the United States would need to play in rebuilding the police and generally maintaining order.
Before the war, the Bush administration dismissed as unnecessary a plan backed by the Justice Department to rebuild the police force by deploying thousands of American civilian trainers. Current and former administration officials said they were relying on a Central Intelligence Agency assessment that said the Iraqi police were well trained. The C.I.A. said its assessment conveyed nothing of the sort.
After Baghdad fell, when the majority of Iraqi police officers abandoned their posts, a second proposal by a Justice Department team calling for 6,600 police trainers was reduced to 1,500, and then never carried out. During the first eight months of the occupation — as crime soared and the insurgency took hold — the United States deployed 50 police advisers in Iraq.
Against the objections of Colin L. Powell, then the secretary of state, the long-range plan was eventually reduced to 500 trainers. The result was a police captain from North Carolina having 40 Americans to train 20,000 Iraqi police across four provinces in southern Iraq.
A Pentagon probe into the death of Iraqi civilians last November in the Iraqi city of Haditha will show that U.S. Marines "killed innocent civilians in cold blood," a U.S. lawmaker said Wednesday.Probe Finds Marines Killed Unarmed Iraqi Civilians:
From the beginning, Iraqis in the town of Haditha said U.S. Marines deliberately killed 15 unarmed Iraqi civilians, including seven women and three children.
...
On Wednesday, Rep. John Murtha, D-Pa., said the accounts are true.
...
On Nov. 20, U.S. Marines spokesman Capt. Jeffrey Pool issued a statement saying that on the previous day a roadside bomb had killed 15 civilians and a Marine. In a later gunbattle, U.S. and Iraqi troops killed eight insurgents, he said.
U.S. military officials later confirmed that the version of events was wrong.
Murtha, a vocal opponent of the war in Iraq, said at a news conference Wednesday that sources within the military have told him that an internal investigation will show that "there was no firefight, there was no IED (improvised explosive device) that killed these innocent people. Our troops overreacted because of the pressure on them, and they killed innocent civilians in cold blood."
Marines from Camp Pendleton wantonly killed unarmed Iraqi civilians, including women and children, and then tried to cover up the slayings in the insurgent stronghold of Haditha, military investigations have found.Springtime for Killing in Afghanistan:
Officials who have seen the findings of the investigations said the filing of criminal charges, including some murder counts, was expected, which would make the Nov. 19 incident the most serious case of alleged U.S. war crimes in Iraq.
An administrative inquiry overseen by Army Maj. Gen. Eldon Bargewell found that several infantry Marines fatally shot as many as 24 Iraqis and that other Marines either failed to stop them or filed misleading or blatantly false reports.
TO most Americans, Afghanistan has been a war of great clarity, the opposite of the war in Iraq with all its troubles and cloudy origins.Gonzales Said He Would Quit in Raid Dispute:
...
Or so Americans thought.
In the last six weeks, a resurgent Taliban has surprised the Americans with the ferocity of its annual spring offensive and set some officials here to worrying that the United States might become tied down in a prolonged battle as control slips away from the central government — in favor of the movement that harbored Al Qaeda before 2001. And the number of American troops has quietly risen, not fallen.
"Afghanistan is the sleeper crisis of this summer," says John J. Hamre, who was deputy defense secretary from 1997 to 1999.
Not only have officials been surprised by the breadth of the militants' presence and the brazenness of their suicide attacks, roadside bombings and assaults by large units. They have also had to face up to the formidable entrenched obstacles to transforming Afghan society: the deep rivalries among ethnic groups, warlords and tribal leaders; the history of civil war; the trouble central governments have in extending their writ beyond the capital; and the hostility toward efforts to attack poppy growing and drug smuggling, which give many a livelihood.
Attorney General Alberto R. Gonzales, the F.B.I. director, Robert S. Mueller III, and senior officials and career prosecutors at the Justice Department told associates this week that they were prepared to quit if the White House directed them to relinquish evidence seized in a bitterly disputed search of a House member's office, government officials said Friday.Justice Dept. Seeks to Block Suits on Spying:
...
Tensions were especially high because officials at the Justice Department and the F.B.I. viewed the Congressional protest, led by Speaker J. Dennis Hastert and House Republicans, as largely a proxy fight for battles likely to come over criminal investigations into other Republicans in Congress.
The Bush administration has asked federal judges in New York and Michigan to dismiss two lawsuits filed over the National Security Agency's domestic eavesdropping program, saying litigating them would jeopardize state secrets.House Panel Backs Net Access Bill:
...
John D. Negroponte, the director of national intelligence, invoked the state secrets privilege, writing that disclosure would cause "exceptionally grave damage" to national security. The administration laid out some of its supporting arguments in classified memos, filed under seal.
The motion, widely anticipated, involves two cases challenging an N.S.A. program that allows investigators to eavesdrop on Americans who communicate by phone or e-mail with people outside the country suspected of terrorist ties.
A U.S. House panel Thursday voted to bar high-speed Internet providers from charging companies such as Google Inc. for priority access to their networks.
The "net neutrality" bill, approved in a 20-13 vote, would prevent phone and cable companies such as AT&T Inc. and Comcast Corp. from using their dominance in the broadband market to control online content, Judiciary Committee members said.
Friday, May 26, 2006
It is over.
I'm done. All the papers have their red numbers written on them, and all the ID numbers have little grades by them. My desk is even relatively clean.
Today hasn't been quite as savorable as the end of some prior semesters (though it was better than last semester's), primarily because my summer field course starts up next week. This year's field course will be much like last year's; the focus will be a week at a field site up in Canada. So, after turning in my grades (and, I'll admit, going to a departmental end-of-the-semester party), I had to work on getting field gear ready, e-mailing my students, and preparing my syllabus.
However, I'm not complaining. It's the end of the semester, I won't have to grade another exam for more than three months, and within a week I'll be in Canada. My cortisol levels are already at a 16-week low.
Today hasn't been quite as savorable as the end of some prior semesters (though it was better than last semester's), primarily because my summer field course starts up next week. This year's field course will be much like last year's; the focus will be a week at a field site up in Canada. So, after turning in my grades (and, I'll admit, going to a departmental end-of-the-semester party), I had to work on getting field gear ready, e-mailing my students, and preparing my syllabus.
However, I'm not complaining. It's the end of the semester, I won't have to grade another exam for more than three months, and within a week I'll be in Canada. My cortisol levels are already at a 16-week low.
Tuesday, May 23, 2006
A bit of bragging
I'm sorry to disappoint all the other teachers out there, but I do have a minor announcement to make: my students are the best around.
In the past week I've had optional review sessions for both my lecture and labs, and even though it's finals week and the students are going insane (thanks in no small part to my course), more than 75% of the class attended both reviews. And not only did they attend, but they came armed with questions galore, and just kept peppering me with them. And they've also been keeping it up after hours, as whenever I log onto my IMs I seem to end up with three or four conversations going at once. It's been great fun.
In the past week I've had optional review sessions for both my lecture and labs, and even though it's finals week and the students are going insane (thanks in no small part to my course), more than 75% of the class attended both reviews. And not only did they attend, but they came armed with questions galore, and just kept peppering me with them. And they've also been keeping it up after hours, as whenever I log onto my IMs I seem to end up with three or four conversations going at once. It's been great fun.
Monday, May 22, 2006
Links
The past week was as busy as I expected, and this coming one is looking to be about the same. However, if all goes well (translate: I dedicate enough time to grading), there's a chance I'll have my grades turned in by Friday night. Oh my, that felt good to type.
Here are a few links to keep everyone occupied:
Orac posted on the recent vitamin study finding that taking multivitamins wasn't beneficial, and also linked to a post by Afarensis about a city preventing unmarried parents from living together.
Dean Dad asked his readers whether requiring a year of language to graduate from college is a good thing.
PZ posted a picture of the glass octopus (wow!) and a secret picture of the real PZ Myers. He also posted on the components of human milk, and then described research that appears to conclude that mammalian breasts first evolved as an immunoprotective structure:
Here are a few links to keep everyone occupied:
Orac posted on the recent vitamin study finding that taking multivitamins wasn't beneficial, and also linked to a post by Afarensis about a city preventing unmarried parents from living together.
Dean Dad asked his readers whether requiring a year of language to graduate from college is a good thing.
PZ posted a picture of the glass octopus (wow!) and a secret picture of the real PZ Myers. He also posted on the components of human milk, and then described research that appears to conclude that mammalian breasts first evolved as an immunoprotective structure:
[T]he mammalian breast first evolved as an immunoprotective gland that produced bacteriocidal secretions to protect the skin and secondarily eggs and infants, and that lactation is a highly derived kind of inflammation response. That mammary glands may have had their origin as inflamed glands suppurating mucus may not be the most romantic image to arise in a scientific study ...Anyone want a glass of milk?
Sunday, May 21, 2006
Baked macaroni and cheese
Baked macaroni and cheese needs no explanation; it's the classic American comfort food with the perfect combination of creaminess and cheesiness complimented with a browned, crispy top. If all you've ever had is boxed (or stove-top) macaroni and cheese, you should make this recipe next time you need some culinary comforting.
I learned to love macaroni and cheese thanks to my mom, as it was one of two dishes we would cook together whenever my stepfather was out of town. This recipe is virtually identical to the one my mom and I used to make, and since my SO and I just cooked it today, it's this week's end-of-the-week recipe blogging post.
1 pound dry pasta (macaroni, penne, pennette, or other)
6 tablespoons unsalted butter (plus a bit more to grease the pan)
6 tablespoons flour
3 3/4 cup warmed milk
1/2 teaspoon freshly ground black pepper
~1/8 teaspoon (a pinch) cayenne
1 teaspoon kosher salt (plus about a tablespoon more for the pasta water)
4 cups grated cheddar cheese (2 cups for the cheese sauce, 2 cups to put in the pan)
For this recipe you need to cook the pasta and make a cheese sauce, then combine them before baking. We often cook the pasta and make the cheese sauce simultaneously, and it's probably ideal (but not necessary) to time it so the cheese sauce and pasta are done at the same time.
Cooking the pasta
1. Fill a large pot with enough water to cover the pasta (at least 6 quarts), and bring to a boil.
2. Once the water is boiling, add the pasta and about 1 tablespoon kosher salt. Stir immediately after adding.
3. Cook for the recommended time on the package, testing the pasta regularly (by tasting it). Do not remove the pasta until it is al dente (just slightly chewy inside); depending on the brand, your pasta may be al dente before, at, or after the recommended cooking time on the package. Don't cook pasta solely by the time printed on the package. Drain the pasta when cooked; do not rinse after draining.
Making the cheese sauce
0. Heat the milk in the microwave (or in a small saucepan over medium heat), but do not bring it to a boil.
1. Melt 6 tablespoons butter in a small non-stick pot over medium-high heat.
2. Add the flour, and, stirring constantly, cook until the flour begins to brown and starts to smell nutty/toasty (probably around 5 minutes).
3. Add the black pepper, cayenne, and salt, and stir.
4. Reduce the heat to medium low, and add the warmed milk to the flour mixture in three or four batches, whisking constantly until smooth.
5. Once the milk has been added, cook, whisking constantly, for 5 minutes, at the end of which time the sauce should be somewhat thickened.
6. Add 2 cups of the cheese (we often add it in two or three batches) and stir until all the cheese is melted.
Assembling and baking the dish
0. Preheat your oven to 350F.
1. Lightly butter the bottom and sides of a 9x13" baking dish (we alternate between using a glass and a silicone baking dish; both work well).
2. Mix the cooked pasta and cheese sauce in a large, heat-proof bowl. Test the salt level, and add more if desired.
3. Layer the grated cheese and pasta in the buttered pan, starting and ending with cheese. The layers should be (from bottom to top):
5. If the top isn't browned enough for your liking at the end of the 30 minutes, broil the dish for a minute or two. To do this turn your oven to its broil setting, adjust your baking rack so that the top of the dish is about 3 inches away from the burner, and put the dish under the broiler. Keep the oven propped open a few inches so you can watch the top brown, and remove the dish from the oven when it's browned to your liking. Watch the dish constantly while it's broiling, as it can go from nicely browned to charred very quickly.
6. Let cool for at least 15 minutes before serving.
Notes:
While the title of the recipe is "macaroni and cheese," nothing says you have to use macaroni in the dish. In fact, we often use penne or pennette. White pepper is traditionally used instead of black pepper (since it doesn't stand out against the sauce), but it tastes just as good with black pepper.
This dish reheats well in a preheated 350F oven; just put the remainder in the oven in a baking dish or on an oven-safe plate, and bake until it's warm (~5-10 minutes, but it depends on the mass and surface-area to volume ratio of the amount you're reheating).
If you have a low salt tolerance, you might want to reduce the amount of salt added to the sauce.
This recipe is modified from one in Chronicle Books (2002), though it's functionally identical to the macaroni and cheese my mom and I made way back when. Chronicle Books suggests pouring 1/2 cup heavy cream on top of the dish before baking; we've made it both ways, and find that the cream doesn't noticeably change the flavor or texture of the dish (yes, it's shocking - we've actually reduced the amount of cream added to something). However, if you're feeding the dish to someone who desperately needs calories, feel free to pour it on.
Reference:
Chronicle Books, ed. 2002. From Our House to Yours: Comfort food to give and share. Chronicle books, San Francisco. p. 63.
[Updated July 8, 2006 to add reheating instructions.]
I learned to love macaroni and cheese thanks to my mom, as it was one of two dishes we would cook together whenever my stepfather was out of town. This recipe is virtually identical to the one my mom and I used to make, and since my SO and I just cooked it today, it's this week's end-of-the-week recipe blogging post.
1 pound dry pasta (macaroni, penne, pennette, or other)
6 tablespoons unsalted butter (plus a bit more to grease the pan)
6 tablespoons flour
3 3/4 cup warmed milk
1/2 teaspoon freshly ground black pepper
~1/8 teaspoon (a pinch) cayenne
1 teaspoon kosher salt (plus about a tablespoon more for the pasta water)
4 cups grated cheddar cheese (2 cups for the cheese sauce, 2 cups to put in the pan)
For this recipe you need to cook the pasta and make a cheese sauce, then combine them before baking. We often cook the pasta and make the cheese sauce simultaneously, and it's probably ideal (but not necessary) to time it so the cheese sauce and pasta are done at the same time.
Cooking the pasta
1. Fill a large pot with enough water to cover the pasta (at least 6 quarts), and bring to a boil.
2. Once the water is boiling, add the pasta and about 1 tablespoon kosher salt. Stir immediately after adding.
3. Cook for the recommended time on the package, testing the pasta regularly (by tasting it). Do not remove the pasta until it is al dente (just slightly chewy inside); depending on the brand, your pasta may be al dente before, at, or after the recommended cooking time on the package. Don't cook pasta solely by the time printed on the package. Drain the pasta when cooked; do not rinse after draining.
Making the cheese sauce
0. Heat the milk in the microwave (or in a small saucepan over medium heat), but do not bring it to a boil.
1. Melt 6 tablespoons butter in a small non-stick pot over medium-high heat.
2. Add the flour, and, stirring constantly, cook until the flour begins to brown and starts to smell nutty/toasty (probably around 5 minutes).
3. Add the black pepper, cayenne, and salt, and stir.
4. Reduce the heat to medium low, and add the warmed milk to the flour mixture in three or four batches, whisking constantly until smooth.
5. Once the milk has been added, cook, whisking constantly, for 5 minutes, at the end of which time the sauce should be somewhat thickened.
6. Add 2 cups of the cheese (we often add it in two or three batches) and stir until all the cheese is melted.
Assembling and baking the dish
0. Preheat your oven to 350F.
1. Lightly butter the bottom and sides of a 9x13" baking dish (we alternate between using a glass and a silicone baking dish; both work well).
2. Mix the cooked pasta and cheese sauce in a large, heat-proof bowl. Test the salt level, and add more if desired.
3. Layer the grated cheese and pasta in the buttered pan, starting and ending with cheese. The layers should be (from bottom to top):
- 1/2 cup cheese on the bottom of the pan
- 1/3 of the pasta and cheese sauce mixture
- 1/2 cup cheese
- 1/3 of the pasta and cheese sauce mixture
- 1/2 cup cheese
- the last 1/3 of the pasta and cheese sauce mixture
- the last 1/2 cup of cheese on top
5. If the top isn't browned enough for your liking at the end of the 30 minutes, broil the dish for a minute or two. To do this turn your oven to its broil setting, adjust your baking rack so that the top of the dish is about 3 inches away from the burner, and put the dish under the broiler. Keep the oven propped open a few inches so you can watch the top brown, and remove the dish from the oven when it's browned to your liking. Watch the dish constantly while it's broiling, as it can go from nicely browned to charred very quickly.
6. Let cool for at least 15 minutes before serving.
Notes:
While the title of the recipe is "macaroni and cheese," nothing says you have to use macaroni in the dish. In fact, we often use penne or pennette. White pepper is traditionally used instead of black pepper (since it doesn't stand out against the sauce), but it tastes just as good with black pepper.
This dish reheats well in a preheated 350F oven; just put the remainder in the oven in a baking dish or on an oven-safe plate, and bake until it's warm (~5-10 minutes, but it depends on the mass and surface-area to volume ratio of the amount you're reheating).
If you have a low salt tolerance, you might want to reduce the amount of salt added to the sauce.
This recipe is modified from one in Chronicle Books (2002), though it's functionally identical to the macaroni and cheese my mom and I made way back when. Chronicle Books suggests pouring 1/2 cup heavy cream on top of the dish before baking; we've made it both ways, and find that the cream doesn't noticeably change the flavor or texture of the dish (yes, it's shocking - we've actually reduced the amount of cream added to something). However, if you're feeding the dish to someone who desperately needs calories, feel free to pour it on.
Reference:
Chronicle Books, ed. 2002. From Our House to Yours: Comfort food to give and share. Chronicle books, San Francisco. p. 63.
[Updated July 8, 2006 to add reheating instructions.]
Thursday, May 18, 2006
Great science headlines of the world
My SO spotted this headline on CNN a few days ago:
Now, what does that headline mean? My guess is that due to all the anti-smoking literature available, most people will immediately pair the group "nonsmoking men" with "smoking men", and thus think that the article is reporting that smoking really isn't all that bad for you.
It turns out that the study being reported on (Thun et al. 2006) compares cancer rates of nonsmoking men to those of nonsmoking women; CNN's first two paragraphs clear this up quickly:
So, a more accurate headline would have been, "Nonsmoking women not more likely to die of cancer than nonsmoking men." Guess that wouldn't have gotten as many clickthroughs.
Thun MJ, SJ Henley, D Burns, A Jemal, TG Shanks, and EE Calle. 2006. Lung Cancer Death Rates in Lifelong Nonsmokers. J Natl Cancer Inst 98:691-699. (Abstract)
Now, what does that headline mean? My guess is that due to all the anti-smoking literature available, most people will immediately pair the group "nonsmoking men" with "smoking men", and thus think that the article is reporting that smoking really isn't all that bad for you.
It turns out that the study being reported on (Thun et al. 2006) compares cancer rates of nonsmoking men to those of nonsmoking women; CNN's first two paragraphs clear this up quickly:
Lung cancer isn't common in people who never smoked. But when they do get it, doctors have long thought that women were more likely to die than men. New research suggests the opposite.OK, so now everything looks clear - the study is actually showing that nonsmoking men are more likely to die of cancer than nonsmoking women, contrary to popular belief. Well, once again the CNN article appears to be misrepresenting things, as the summary of the journal article on the journal's homepage reports the following:
Analyzing medical records of nearly 1 million people, American Cancer Society researchers reported Tuesday that men who never used cigarettes actually had slightly higher death rates from lung cancer than women who never smoked.
Women nonsmokers are equally likely to die from lung cancer as men, but nonsmoking African American women may be at higher risk of lung cancer death than white women.The abstract of the article does indeed report that men have a higher reported incidence of cancer, but my guess is that this higher incidence is not statistically significant (I don't have access to the full text of the article, so can't confirm this), and thus shouldn't be reported on.
So, a more accurate headline would have been, "Nonsmoking women not more likely to die of cancer than nonsmoking men." Guess that wouldn't have gotten as many clickthroughs.
Thun MJ, SJ Henley, D Burns, A Jemal, TG Shanks, and EE Calle. 2006. Lung Cancer Death Rates in Lifelong Nonsmokers. J Natl Cancer Inst 98:691-699. (Abstract)
Monday, May 15, 2006
The end is coming ...
You might think that since some lucky bums are done for the semester, I'm also done. Unfortunately, I still have a few weeks to go. And, since in the coming few weeks I'll be grading piles of papers and exams in a mad dash to the end, and then starting my summer field course almost immediately after the end of the semester, I'm afraid that I'll likely be a bit distracted from regular posting here. I apologize for any long breaks.
In the meantime, I suggest amusing yourself by reading about unauthorized wiretaps in the garden (a post by Carl Zimmer about caterpillars avoiding parasitic wasps that are attracted by signals from plants the caterpillars are eating) and helping Profgrrrrl figure out how she should electronically submit her manuscript. And, if you don't want to amuse yourself, go read about the Bush administration tracking calls made by reporters.
In the meantime, I suggest amusing yourself by reading about unauthorized wiretaps in the garden (a post by Carl Zimmer about caterpillars avoiding parasitic wasps that are attracted by signals from plants the caterpillars are eating) and helping Profgrrrrl figure out how she should electronically submit her manuscript. And, if you don't want to amuse yourself, go read about the Bush administration tracking calls made by reporters.
Quick and easy chewy brownies
My SO and I prefer soft, chewy brownies, but were frustrated with many of our initial attempts at making them - they typically ended up too hard and crunchy, too cakey, or underbaked. Then we found this recipe on King Arthur Flour's site a few years ago, and with a few modifications it's consistently made (what we consider to be) great rich, chewy, chocolatey brownies. Not only are the brownies delicious, but they're also incredibly easy to make: they require one bowl, the only chocolate added is cocoa powder, and the entire process should take about half an hour from start to nibbling on hot-out-of-the-oven brownies. We agree with King Arthur Flour that these are "perfect for that potluck you forgot about till the last minute." Since we just made these last night, they're this week's end-of-the-week recipe blogging post.
2 cups granulated sugar
3/4 cup cocoa powder
1 cup flour
1/4 teaspoon salt
1/4 teaspoon baking powder
3 eggs
8 tablespoons (1 stick) unsalted butter, melted
1/4 cup vegetable oil
2 teaspoons vanilla
1 1/4 cups coarsely chopped pecans
0. Preheat the oven to 375F, and lightly grease the bottom and sides of a 9x13" glass baking dish.
1. Mix the sugar and cocoa powder in a large bowl until there are no large lumps of cocoa powder.
2. Add the flour, salt, and baking powder to the bowl and mix.
3. Add the eggs, melted butter, vegetable oil, and vanilla; mix until well combined.
4. Mix in the pecans (we typically use whole pecans and break them between our fingers as we add them), and then pour the batter into the greased pan. Spread the batter with a spatula so it's level, and bake for 20 minutes.
Notes:
We prefer pecans in the brownies, but they also taste fine with a mix of pecans and walnuts, just walnuts, or no nuts at all. We always use a glass baking dish; if you use a metal pan, the cooking time might vary.
Reference:
King Arthur Flour, "Wicked Easy Fudge Brownies." (link)
2 cups granulated sugar
3/4 cup cocoa powder
1 cup flour
1/4 teaspoon salt
1/4 teaspoon baking powder
3 eggs
8 tablespoons (1 stick) unsalted butter, melted
1/4 cup vegetable oil
2 teaspoons vanilla
1 1/4 cups coarsely chopped pecans
0. Preheat the oven to 375F, and lightly grease the bottom and sides of a 9x13" glass baking dish.
1. Mix the sugar and cocoa powder in a large bowl until there are no large lumps of cocoa powder.
2. Add the flour, salt, and baking powder to the bowl and mix.
3. Add the eggs, melted butter, vegetable oil, and vanilla; mix until well combined.
4. Mix in the pecans (we typically use whole pecans and break them between our fingers as we add them), and then pour the batter into the greased pan. Spread the batter with a spatula so it's level, and bake for 20 minutes.
Notes:
We prefer pecans in the brownies, but they also taste fine with a mix of pecans and walnuts, just walnuts, or no nuts at all. We always use a glass baking dish; if you use a metal pan, the cooking time might vary.
Reference:
King Arthur Flour, "Wicked Easy Fudge Brownies." (link)
Sunday, May 14, 2006
Political news of the week, take 13
[See also: political news of the week takes 12, 11, 10, 9b, 9a, 8, 7, 6, 5, 4, 3, 2, and 1.]
NSA has created a massive database of Americans' phone calls: For more, see my recent post.
Cheney Pushed U.S. to Widen Eavesdropping: An article in the New York Times about the NSA wiretapping program (as opposed to the NSA phone-call database program, discussed in the links above):
NSA has created a massive database of Americans' phone calls: For more, see my recent post.
Cheney Pushed U.S. to Widen Eavesdropping: An article in the New York Times about the NSA wiretapping program (as opposed to the NSA phone-call database program, discussed in the links above):
In the weeks after the Sept. 11 attacks, Vice President Dick Cheney and his top legal adviser argued that the National Security Agency should intercept purely domestic telephone calls and e-mail messages without warrants in the hunt for terrorists, according to two senior intelligence officials.GOP Reaches Accord on Tax Cut Package:
But N.S.A. lawyers, trained in the agency's strict rules against domestic spying and reluctant to approve any eavesdropping without warrants, insisted that it should be limited to communications into and out of the country, said the officials, who were granted anonymity to discuss the debate inside the Bush administration late in 2001.
The N.S.A.'s position ultimately prevailed. But just how Gen. Michael V. Hayden, the director of the agency at the time, designed the program, persuaded wary N.S.A. officers to accept it and sold the White House on its limits is not yet fully clear.
...
The official said General Hayden appeared particularly concerned about ensuring that one end of each conversation was outside the United States. For his employees at the N.S.A., whose mission is foreign intelligence, avoiding purely domestic eavesdropping appears to have been crucial.
...
And one government official, who had access to intelligence from the intercepts that he said he would speak about only if granted anonymity, believes that some of the purely domestic eavesdropping in the program's early phase was intentional. No other officials have made that claim.
President Bush and other officials have denied that the program monitors any domestic calls. They have, however, generally stated their comments in the present tense, leaving open the question of whether domestic calls may have been captured before the program's rules were fully established.
House and Senate Republican leaders reached agreement Tuesday on a $70-billion tax cut package that would extend some expiring tax breaks and authorize new ones, particularly for upper-income taxpayers.F.B.I.'s Focus on Public Corruption Includes 2,000 Investigations:
...
The bill would extend lowered tax rates on investment income, now scheduled to expire after 2008, for an additional two years. For the current year, it would blunt the impact of the alternative minimum tax on about 15 million taxpayers.
...
The bill's chief negotiators — Sen. Charles E. Grassley (R-Iowa), chairman of the Senate Finance Committee, and Rep. Bill Thomas (R-Bakersfield), chairman of the House Ways and Means Committee — said they had reached agreement on provisions of a second tax measure, which would cost up to $36 billion over five years.
The decision to split tax legislation into two bills is a result of the congressional budget process. Under arcane budget rules, only $70 billion in tax cuts can be considered in the Senate using a "fast track" procedure that prevents a filibuster and allows passage by a simple majority.
Of the Senate's 100 members, 55 are Republicans — but some of them, fearing the effect on the deficit and the disproportionate benefit to the wealthiest taxpayers, are reluctant to extend the lowered rates on income from dividends and profits from the sale of investments, known as capital gains. For example, Sen. Olympia J. Snowe (R-Maine), a Finance Committee member, said she would oppose the bill as written by Grassley and Thomas.
The second bill will not benefit from the same fast-track procedures, and will need 60 votes in the Senate.
To encourage passage of the second bill, Grassley and Thomas loaded it with retroactive extensions of the most popular tax breaks that expired at the beginning of the year, including a research and development tax credit for businesses, a deduction for certain college tuition payments, and benefits for teachers who pay for classroom supplies themselves.
A post-9/11 effort by the F.B.I. to concentrate on public corruption now includes more than 2,000 investigations under way, highlighted by the Jack Abramoff lobbying inquiry, the racketeering and fraud conviction of former Gov. George Ryan of Illinois, and the multipronged corruption probes after the guilty plea by Randy Cunningham, a former Republican House member from San Diego, bureau officials said.House Panel Challenges Smithsonian: A New York Times article on the a House committee's response to the Smithsonian deal that was in a prior political links post.
As one of the Bush administration's least known anticrime efforts, the F.B.I. initiative has yielded an unexpectedly rich array of cases. The results suggest that wrongdoing by public officials at all levels of government is deeply rooted and widespread. Several of the highest profile cases in which the F.B.I. played an active role involve Republicans.
Bureau officials believe that the investment in corruption cases is easily worth the cost. In 2004 and 2005, more than 1,060 government employees were convicted of corrupt activities, including 177 federal officials, 158 state officials, 360 local officials and 365 police officers, according to F.B.I. statistics. The number of convictions rose 27 percent from 2004 to 2005.
Bluntly rejecting the Smithsonian Institution's defense of its recent television deal with Showtime Networks, the House Appropriations Committee yesterday demanded further information on the contract, which members of the committee have said limits access and "may be incompatible with the trust placed in the Smithsonian."Flu Preparedness Would Make [California] a Leader:
The committee also cut $15 million from the Smithsonian's proposed budget and sought a cap on salaries.
The committee's actions came one day after the Smithsonian's governing board asserted, in a letter to the Appropriations subcommittee that oversees its finances, that the deal did not restrict access to its collections, as claimed by critics. The letter also rebuffed the subcommittee's suggestion that it conduct public hearings on business ventures that affect access to its collections.
Gov. Arnold Schwarzenegger's proposed $400-million investment in pandemic flu and disaster preparedness — by far the largest amount any state has devoted to the cause — would vault California from a laggard to a national leader in one stroke, healthcare experts said Friday.
...
Provisions in the governor's plan, which is subject to two-thirds approval by the Legislature, include:
Buying nearly 7,200 ventilators, at a cost of nearly $100 million — almost double the number the federal government is to purchase for the entire nation.
Allocating $164 million to help hospitals open and supply equipment for tens of thousands of extra beds in an emergency.
Paying $53 million for nearly 3.7 million doses of anti-flu drugs, $50 million for protective respiratory masks and $12 million for two tent-like mobile hospitals — complete with operating rooms, intensive-care units and isolation wards — that each could handle 200 patients.
...
Shewry said health officials came up with the proposal after reviewing results from California's first comprehensive survey of hospital resources, and comparing the gaps to federal guidelines of what the state needs.
They found that California has 72,000 licensed and staffed hospital beds, and could find an additional 17,300 in an emergency. But a pandemic flu would require as many as 130,700 beds at its peak.
Officials also found that the number of ventilators the state had was woefully inadequate — only 7,183, yet the state would need about 34,000 in a pandemic. The additional purchase would not entirely cover the state's needs, but it would double the state's supply, Shewry said.
Thursday, May 11, 2006
California budget revision coming soon
According to this LA Times article, Governor Schwarzenegger is going to submit a revised budget this Friday that includes "plans to retire a large chunk of the state's debt and boost education funding with more than $5 billion in unexpected revenue from surging tax receipts." On the surface this sounds like a good start to fixing the state's school funding problems (and will likely be far better than Schwarzenegger's May budget revision from last year, where education was almost entirely overlooked), but as always the details will be critical.
[For more on California's school funding issues, see my posts from March (1, 2, 3, 4, 5), April (1, 2), May (1, 2), and June (1) of last year]
[For more on California's school funding issues, see my posts from March (1, 2, 3, 4, 5), April (1, 2), May (1, 2), and June (1) of last year]
The government is tracking you (in case you didn't already know)
[This post has been updated; see below for more.]
An article in USA Today reports that the NSA has created a massive database of Americans' phone calls:
And, as with the warrantless wiretapping program, it appears that this program is illegal:
[Update: ThinkProgress has more information on why the program is likely illegal:]
An article in USA Today reports that the NSA has created a massive database of Americans' phone calls:
The National Security Agency has been secretly collecting the phone call records of tens of millions of Americans, using data provided by AT&T, Verizon and BellSouth, people with direct knowledge of the arrangement told USA TODAY.AT&T, BellSouth, Verizon, and SBC are all being paid by the NSA to participate; Qwest is "the lone holdout among the big telecommunications companies."
The NSA program reaches into homes and businesses across the nation by amassing information about the calls of ordinary Americans — most of whom aren't suspected of any crime.
...
The NSA's domestic program, as described by sources, is far more expansive than what the White House has acknowledged. Last year, Bush said he had authorized the NSA to eavesdrop — without warrants — on international calls and international e-mails of people suspected of having links to terrorists when one party to the communication is in the USA. Warrants have also not been used in the NSA's efforts to create a national call database.
In defending the previously disclosed program, Bush insisted that the NSA was focused exclusively on international calls. "In other words," Bush explained, "one end of the communication must be outside the United States."
As a result, domestic call records — those of calls that originate and terminate within U.S. borders — were believed to be private.
Sources, however, say that is not the case. With access to records of billions of domestic calls, the NSA has gained a secret window into the communications habits of millions of Americans. Customers' names, street addresses and other personal information are not being handed over as part of NSA's domestic program, the sources said. But the phone numbers the NSA collects can easily be cross-checked with other databases to obtain that information.
And, as with the warrantless wiretapping program, it appears that this program is illegal:
Under Section 222 of the Communications Act, first passed in 1934, telephone companies are prohibited from giving out information regarding their customers' calling habits: whom a person calls, how often and what routes those calls take to reach their final destination. Inbound calls, as well as wireless calls, also are covered.Bush's response (as quoted by CNN) to this report was, "We are not mining or trolling through the personal lives of innocent Americans." If tracking every single call millions of Americans make isn't rooting through "innocent Americans'" personal lives, I'd like to know what is.
The financial penalties for violating Section 222, one of many privacy reinforcements that have been added to the law over the years, can be stiff. The Federal Communications Commission, the nation's top telecommunications regulatory agency, can levy fines of up to $130,000 per day per violation, with a cap of $1.325 million per violation. The FCC has no hard definition of "violation." In practice, that means a single "violation" could cover one customer or 1 million.
[Update: ThinkProgress has more information on why the program is likely illegal:]
1. It violates the Stored Communications Act. The Stored Communications Act, Section 2703(c), provides exactly five exceptions that would permit a phone company to disclose to the government the list of calls to or from a subscriber: (i) a warrant; (ii) a court order; (iii) the customer’s consent; (iv) for telemarketing enforcement; or (v) by “administrative subpoena.” The first four clearly don’t apply. As for administrative subpoenas, where a government agency asks for records without court approval, there is a simple answer – the NSA has no administrative subpoena authority, and it is the NSA that reportedly got the phone records.[Update 2: And the LA Times has come up with another law that this program appears to violate:]2. The penalty for violating the Stored Communications Act is $1000 per individual violation. Section 2707 of the Stored Communications Act gives a private right of action to any telephone customer “aggrieved by any violation.” If the phone company acted with a “knowing or intentional state of mind,” then the customer wins actual harm, attorney’s fees, and “in no case shall a person entitled to recover receive less than the sum of $1,000.”
(The phone companies might say they didn’t “know” they were violating the law. But USA Today reports that Qwest’s lawyers knew about the legal risks, which are bright and clear in the statute book.)
3. The Foreign Intelligence Surveillance Act doesn’t get the telcos off the hook. According to USA Today, the NSA did not go to the FISA court to get a court order. And Qwest is quoted as saying that the Attorney General would not certify that the request was lawful under FISA. So FISA provides no defense for the phone companies, either.
The Electronic Communications Privacy Act of 1986 was passed when cellphones and the Internet were emerging as new forms of communication. Section 2702 of the law says the providers of "electronic communications … shall not knowingly divulge a record or other information pertaining to a subscriber or customer … to any government entity."
Companies that violate the law are subject to being sued and paying damages of at least $1,000 per violation per customer.
...
[In 1967], the [US Supreme] court said a government agent listening to a private phone call was the equivalent of a search. That ruling, in Katz vs. United States, required police and federal agents thereafter to obtain a search warrant from a judge before they wiretapped a phone.
Still, phone records are not the same as phone conversations, and the high court refused to extend the privacy protections of the 4th Amendment to a list of dialed phone numbers.
"We doubt that people in general entertain any actual expectation of privacy in the [phone] number they dial," the court said in the 1979 case of Smith vs. Maryland. This ruling gave the police freedom to obtain phone records without a warrant.
To close that loophole, Congress enacted the Electronic Communications Privacy Act, forbidding the phone companies to divulge phone records.
The law includes several exceptions. For example, phone records may be disclosed "with the lawful consent of the customer." Another exception involves "any emergency involving danger of death or serious physical injury." In such a situation, the "provider in good faith" may give the requested phone records to a government official.
Wednesday, May 10, 2006
Viruses and mammalian phylogenetics
Will the virus-based news never cease? A recent article (Kriegs et al. 2006) in PLOS Biology reports on a phylogeny of placental mammals constructed from markers left by retroviruses (retroposons). Carl Zimmer has more background on this technique; suffice to say that using retroposons is an extremely accurate method for reconstructing phylogenies. The resulting phylogeny is below:
"Positions of Retroposed Elements as Landmarks of Evolution on the Bayesian-Based Placental Evolutionary Tree from Murphy et al. The resultant tree is consistent with previous studies in most aspects. Note that the positions of afrotherians and xenarthras have been reversed, based on the presence of two retroposon insertions at node 2. Gray balls represent single insertion events. Supported splitting points are labeled with Arabic numerals. Superordinal clades, in the order shown, were established by Waddell et al. and supported by several major studies, and are labeled with Roman numerals. The taxa shown represent only those from which we sampled LINEs and LTRs. Dotted lines indicate nodes in need of further confirmation. Asterisks represent retroposon evidence from the literature for monophyly of Afrotheria, Primates, Rodentia, and Cetartiodactyla."
I'm quite pleased that this phylogeny supports the idea (seen in other phylogenies as well) that rats and mice are closer (evolutionarily) to humans than dogs or cats (both of which are in Carnivora). Take that, dog and cat lovers!
Kriegs JO, Churakov G, Kiefmann M, Jordan U, Brosius J, et al. (2006) Retroposed Elements as Archives for the Evolutionary History of Placental Mammals. PLoS Biol 4(4): e91 (full-text, PDF)
"Positions of Retroposed Elements as Landmarks of Evolution on the Bayesian-Based Placental Evolutionary Tree from Murphy et al. The resultant tree is consistent with previous studies in most aspects. Note that the positions of afrotherians and xenarthras have been reversed, based on the presence of two retroposon insertions at node 2. Gray balls represent single insertion events. Supported splitting points are labeled with Arabic numerals. Superordinal clades, in the order shown, were established by Waddell et al. and supported by several major studies, and are labeled with Roman numerals. The taxa shown represent only those from which we sampled LINEs and LTRs. Dotted lines indicate nodes in need of further confirmation. Asterisks represent retroposon evidence from the literature for monophyly of Afrotheria, Primates, Rodentia, and Cetartiodactyla."
I'm quite pleased that this phylogeny supports the idea (seen in other phylogenies as well) that rats and mice are closer (evolutionarily) to humans than dogs or cats (both of which are in Carnivora). Take that, dog and cat lovers!
Kriegs JO, Churakov G, Kiefmann M, Jordan U, Brosius J, et al. (2006) Retroposed Elements as Archives for the Evolutionary History of Placental Mammals. PLoS Biol 4(4): e91 (full-text, PDF)
Want to keep a potentially illegal program from being investigated?
All you have to do is prevent the investigators from getting security clearance:
The government has abruptly ended an inquiry into the warrantless eavesdropping program because the National Security Agency refused to grant Justice Department lawyers security clearance.
The Justice Department's Office of Professional Responsibility, or OPR, sent a fax Wednesday to Democratic Rep. Maurice Hinchey of New York saying it was closing its inquiry because without clearance it could not examine department lawyers' role in the program.
"We have been unable to make any meaningful progress in our investigation because OPR has been denied security clearances for access to information about the NSA program," OPR counsel H. Marshall Jarrett wrote to Hinchey. Hinchey's office shared the letter with The Associated Press.
...
Roehrkasse noted the OPR's mission is not to investigate possible wrongdoing in other agencies, but to determine if Justice Department lawyers violated any ethical rules.
Choosing a medical discipline
Many of my students want to be doctors, but aren't yet sure of their preferred specialty; maybe this figure will help:
(Via Orac and The Huffington Post)
(Via Orac and The Huffington Post)
Tuesday, May 09, 2006
Firefox plugins that block ads
Thanks to ScienceBlog's awful tornado ad (and the comments in PZ's post on the topic), I've just found three very nice Firefox plugins:
- Adblock - An extension that prevents most static ads from displaying on web pages (more information on their project page).
- Adblock Filterset.G Updater - A set of filters for Adblock that are automatically updated regularly.
- Flashblock - Replaces all flash objects with a static image that has a play button. If you want to see the animation, click play; if not, the flash animation stays static. This is great for eliminating animated ads from webpages.
Links
This week's going to be another crazy one (as are the next two), so here are some links to keep everyone happy:
But She's a Girl reports on a birthday card's safety warning.
Dylan writes about chemicals that smell like goats (via PZ).
An article by Carl Zimmer in the New York Times on songbirds possibly learning grammar (which should be of interest to SC).
A post by Orac on a case more disturbing than Terry Schiavo, followed by an update on the case.
A post by PZ on the Third of May.
And, to end on a lighter note, Dean Dad instructs us on how to give an IT director fits.
But She's a Girl reports on a birthday card's safety warning.
Dylan writes about chemicals that smell like goats (via PZ).
An article by Carl Zimmer in the New York Times on songbirds possibly learning grammar (which should be of interest to SC).
A post by Orac on a case more disturbing than Terry Schiavo, followed by an update on the case.
A post by PZ on the Third of May.
And, to end on a lighter note, Dean Dad instructs us on how to give an IT director fits.
Monday, May 08, 2006
German-style board games
My SO and I were recently invited by a colleague to spend an evening playing German-style board games. Neither my SO nor I even knew that there was such a genre of games, and had no idea what we were getting into. Now, after playing Settlers of Catan, San Juan, and St. Petersburg, we're wondering why we've never heard of these games before.
Most board games played by Americans seem as though they can be divided into either pure strategy (e.g., Chess, Go, Cathedral, Stratego) or largely luck-based (e.g., Monopoly, Life, Sorry!, Chutes and Ladders) games. In pure strategy games, player skill dictates virtually the entire game (e.g., a novice chess player will always lose to an expert), which makes the games fun only if players have equal skills. Luck-based games, on the other hand, often have extremely limited strategic decisions (in Monopoly the optimal strategy seems as though it could be summed up as "buy as many properties as you can, trying to get a monopoly, until you run out of money"), skill has very little to do with the outcome of the game, and pretty much everything is based on the roll of a die (or draw of a card). In both types of games, the winner of the game can often be predicted long before the end of the game (and sometimes players can be officially eliminated before the end of the game), which can distract from the fun.
German-style board games seem to have found a very enjoyable middle ground between these two extremes. The games have simple rules (we learned how to play each game in about 10 minutes), don't take too much time to play (30-90 minutes per game), require lots of strategic thinking, yet include enough luck so that everyone has the potential to win the game. For example, we were playing against extremely experienced players, yet we were still able to win a game, and never felt like we had no hope of winning.
The Wikipedia has a good summary of German-style board games; here's their list of characteristics common to German-style board games (taken directly from this page):
Most board games played by Americans seem as though they can be divided into either pure strategy (e.g., Chess, Go, Cathedral, Stratego) or largely luck-based (e.g., Monopoly, Life, Sorry!, Chutes and Ladders) games. In pure strategy games, player skill dictates virtually the entire game (e.g., a novice chess player will always lose to an expert), which makes the games fun only if players have equal skills. Luck-based games, on the other hand, often have extremely limited strategic decisions (in Monopoly the optimal strategy seems as though it could be summed up as "buy as many properties as you can, trying to get a monopoly, until you run out of money"), skill has very little to do with the outcome of the game, and pretty much everything is based on the roll of a die (or draw of a card). In both types of games, the winner of the game can often be predicted long before the end of the game (and sometimes players can be officially eliminated before the end of the game), which can distract from the fun.
German-style board games seem to have found a very enjoyable middle ground between these two extremes. The games have simple rules (we learned how to play each game in about 10 minutes), don't take too much time to play (30-90 minutes per game), require lots of strategic thinking, yet include enough luck so that everyone has the potential to win the game. For example, we were playing against extremely experienced players, yet we were still able to win a game, and never felt like we had no hope of winning.
The Wikipedia has a good summary of German-style board games; here's their list of characteristics common to German-style board games (taken directly from this page):
- Variable number of players - The games are designed to be played with a wide ranging group. Typically the minimum number of players is only two or three, and the maximum might be four or five or even more.
- Simple, clever rules - The rules for most games are only a few pages and simple to learn. Novel mechanisms that will be unfamiliar to those brought up on older titles are often incorporated. The "roll-and-move" mechanic of games like Monopoly is almost never seen. If a monetary system is included at all, it is usually very simple.
- No player elimination - The games usually continue until some defined set of criteria is met. At that point, a winner is determined. Players don't get kicked out in midgame by running out of money or armies.
- Heavy player interaction - Players often trade, compete for resources, try to win auctions, or affect one another in other ways.
- Minimize direct conflict - War is rarely a theme. It is often difficult or impossible for one player to destroy other players' pieces or position. Usually you are trying to make your own position stronger or stop other players from growing.
- Mitigated luck - The games usually feature some component of luck to keep the games exciting and varied. However, luck is often balanced against numerous strategic and tactical decisions. A skilled player will win far more than a foolish one.
- Diversity of situations - The combination of unusual rules and randomness is used to achieve a variety of possible situations. The goal is to keep the game interesting and fresh even after it has been played many times.
- Modest length - Games are typically designed to take about an hour, and most will rarely take more than two.
- Attractive - Games are usually well illustrated and have quality board and pieces. Bright coloring, and wood or metal components are not unusual. This does often raise the price (typically between US$20 and US$50).
- A greater emphasis on mechanics over theme. For example, US style game designers will reuse the same mechanics but with a new theme (or make use of licensed themes from books or movies) whereas German style designers will more so strive for new mechanics but often reuse the same theme.
Grading and plagiarism
I have finished my huge pile of grading. It's done. Finally. And I only went through three red pens (because they were old and dried up).
I haven't finished my plagiarism scanning yet, but have already found one plagiarized paper. Of course, considering that I've found at least one plagiarized paper in each of the last 10 semesters, this should surprise no one. It would be so lovely if I could have at least one semester go by without filling out plagiarism report paperwork.
I haven't finished my plagiarism scanning yet, but have already found one plagiarized paper. Of course, considering that I've found at least one plagiarized paper in each of the last 10 semesters, this should surprise no one. It would be so lovely if I could have at least one semester go by without filling out plagiarism report paperwork.
Sunday, May 07, 2006
Political news of the week, take 12
[See also: political news of the week takes 11, 10, 9b, 9a, 8, 7, 6, 5, 4, 3, 2, and 1.]
Bush challenges hundreds of laws - A detailed article in the Boston Globe that documents Bush's attempts at concentrating power by issuing "signing statements."
Bush challenges hundreds of laws - A detailed article in the Boston Globe that documents Bush's attempts at concentrating power by issuing "signing statements."
President Bush has quietly claimed the authority to disobey more than 750 laws enacted since he took office, asserting that he has the power to set aside any statute passed by Congress when it conflicts with his interpretation of the Constitution.Taliban Threat Is Said to Grow in Afghan South:
Among the laws Bush said he can ignore are military rules and regulations, affirmative-action provisions, requirements that Congress be told about immigration services problems, ''whistle-blower" protections for nuclear regulatory officials, and safeguards against political interference in federally funded research.
Legal scholars say the scope and aggression of Bush's assertions that he can bypass laws represent a concerted effort to expand his power at the expense of Congress, upsetting the balance between the branches of government. The Constitution is clear in assigning to Congress the power to write the laws and to the president a duty ''to take care that the laws be faithfully executed." Bush, however, has repeatedly declared that he does not need to ''execute" a law he believes is unconstitutional.
...
Bush is the first president in modern history who has never vetoed a bill, giving Congress no chance to override his judgments. Instead, he has signed every bill that reached his desk, often inviting the legislation's sponsors to signing ceremonies at which he lavishes praise upon their work.
Then, after the media and the lawmakers have left the White House, Bush quietly files ''signing statements" -- official documents in which a president lays out his legal interpretation of a bill for the federal bureaucracy to follow when implementing the new law. The statements are recorded in the federal register.
In his signing statements, Bush has repeatedly asserted that the Constitution gives him the right to ignore numerous sections of the bills -- sometimes including provisions that were the subject of negotiations with Congress in order to get lawmakers to pass the bill. He has appended such statements to more than one of every 10 bills he has signed.
...
In October 2004, five months after the Abu Ghraib torture scandal in Iraq came to light, Congress passed a series of new rules and regulations for military prisons. Bush signed the provisions into law, then said he could ignore them all. One provision made clear that military lawyers can give their commanders independent advice on such issues as what would constitute torture. But Bush declared that military lawyers could not contradict his administration's lawyers.
Other provisions required the Pentagon to retrain military prison guards on the requirements for humane treatment of detainees under the Geneva Conventions, to perform background checks on civilian contractors in Iraq, and to ban such contractors from performing ''security, intelligence, law enforcement, and criminal justice functions." Bush reserved the right to ignore any of the requirements.
Building on a winter campaign of suicide bombings and assassinations and the knowledge that American troops are leaving, the Taliban appear to be moving their insurgency into a new phase, flooding the rural areas of southern Afghanistan with weapons and men.Bush Speaks of Closing Guantánamo Prison:
Each spring with the arrival of warmer weather, the fighting season here starts up, but the scale of the militants' presence and their sheer brazenness have alarmed Afghans and foreign officials far more than in previous years.
"The Taliban and Al Qaeda are everywhere," a shopkeeper, Haji Saifullah, told the commander of American forces in Afghanistan, Lt. Gen. Karl Eikenberry, as the general strolled through the bazaar of this town to talk to people. "It is all right in the city, but if you go outside the city, they are everywhere, and the people have to support them. They have no choice."
The fact that American troops are pulling out of southern Afghanistan in the coming months, and handing matters over to NATO peacekeepers, who have repeatedly stated that they are not going to fight terrorists, has given a lift to the insurgents, and increased the fears of Afghans.
President Bush said yesterday that he would like to close the United States-run prison at Guantánamo Bay, Cuba, a step that has been urged by several foreign leaders. But he said he was awaiting a Supreme Court ruling on where the terrorism suspects held there might be tried.Guard Faces Phase-Out of Combat Role:
...
"Of course Guantánamo is a delicate issue for people," Mr. Bush said, in remarks that were translated by Reuters from a German transcript. "I would like to close the camp and put the prisoners on trial."
"Our top court must still rule on whether they should go before a civil or military court," he continued. "They will get their day in court. One can't say that of the people that they killed."
National Guard troops in Iraq, which once constituted half the Army's fighting force, have been dramatically reduced and could be largely phased out of major combat responsibilities next year as military officials debate their performance and what role they should play in future conflicts.Plan for $100 Gas Rebate Appears to Be Dead:
...
Some active-duty soldiers argue the most capable guardsmen have served in combat support units — military police companies or engineering battalions. In these units, Guard members often had civilian skills that complemented their military training and made them more adept, knowledgeable and flexible than active duty counterparts.
With 351 Guard soldiers killed in Iraq and another 2,867 wounded, many active-duty officers avoid criticizing the force. But some regular Army officers have suggested that many of the Guard units were too cautious, overly concerned with casualties and simply did not have the intensity of training to match the active-duty force. Guard units were not able to as quickly master the difficulties of the counter-insurgency fight, say some Iraq veterans.
"Iraq showed what we have really always known, that the more complex combined arms operations that take extensive training and considerable experience are more difficult for units that get two weeks of training a year," said one Army general, who spoke on condition of anonymity because publicly criticizing the Guard is frowned on in the military. "We need to be honest with ourselves. Six months of preparation does not provide the same foundation as five, 10, 15 years of full-time experience."
A Republican proposal to provide taxpayers with $100 rebates to compensate for higher fuel prices appeared all but dead on Tuesday, with leading Congressional Republicans saying that it had quickly fallen flat.Kaiser Put Kidney Patients at Risk: An LA Times article reporting on Kaiser's new kidney transplant center.
"I just think that trying to satisfy voters with a $100 voucher is insulting," said Representative John A. Boehner of Ohio, the House majority leader. "Over the weekend, I heard about it from my constituents a few times. They thought it was stupid."
In mid-2004, more than 1,500 Kaiser Permanente patients awaiting kidney transplants in Northern California got form letters that forced them to change the course of their treatment.Kaiser Denied Transplants of Ideally Matched Kidneys:
Kaiser would no longer pay for transplants at outside hospitals, even established programs with thousands of successes. Instead, adult patients would be transferred to a new transplant center run by Kaiser itself — the first ever opened by the nation's largest HMO.
...
Kaiser's massive rollout in Northern California endangered patients, forcing them into a fledgling program unprepared to handle the caseload, according to a Times investigation based on statistical analyses, confidential documents and dozens of interviews.
Hundreds of patients were stuck in transplant limbo for months because Kaiser failed to properly handle paperwork. Meanwhile, doctors attempting to build a record of success shied away from riskier organs and patients, slowing the rate of transplants performed.
National transplant regulators apparently did not notice the program's failures, though some were obvious in the statistics the regulators themselves posted on the Internet.
In 2005, the program's first full year, Kaiser performed only 56 transplants, while twice that many people on the waiting list died, according to a Times analysis of national transplant statistics.
At transplant centers statewide, the pattern was the reverse: More than twice as many people received kidneys than died.
Twenty-five Kaiser Permanente patients in Northern California were denied the chance for new kidneys that were nearly perfectly matched to them last year during the troubled start-up of the giant HMO's kidney transplant program in San Francisco, a Times investigation has found.
The patients missed this opportunity because they were in effect stranded between two transplant programs.
Kaiser never properly completed the paperwork to transfer the patients' cases to its program from UC San Francisco Medical Center, which had been under contract to care for them until September 2004. At the same time, Kaiser would not authorize UC San Francisco to continue accepting kidneys and transplanting them into Kaiser patients, according to interviews, internal memos and transplant records.
UC San Francisco transplant officials said they asked Kaiser if they could transplant some of the offered organs and Kaiser representatives told them no, said Dr. Stephen Tomlanovich, medical director of the university's renal transplant service. An e-mail from Tomlanovich to a UC San Francisco colleague in February 2005 confirms his account.
Saturday, May 06, 2006
Some weekend technology reading
This weekend my life is dedicated to grading. As I said on Wednesday, I have a huge backlog of papers, and I have to get through them by next week (so I can be ready for the next deluge of papers). So, there won't be much from me until that's done.
However, to keep everyone happy, here are a few technology articles (via BoingBoing):
The RFID Hacking Underground: A Wired article on how insecure most RFID chips are (including ones used in keycards, libraries, payment services, and even those implanted in humans).
You're the Bad Guy Here: Another Wired article, but this time discussing how Muslims are modding games so that the Americans are the bad guys and Muslims are the good guys.
[Update: BoingBoing reports that the games described in the second article may be a hoax.]
However, to keep everyone happy, here are a few technology articles (via BoingBoing):
The RFID Hacking Underground: A Wired article on how insecure most RFID chips are (including ones used in keycards, libraries, payment services, and even those implanted in humans).
You're the Bad Guy Here: Another Wired article, but this time discussing how Muslims are modding games so that the Americans are the bad guys and Muslims are the good guys.
Battlefield 2 ordinarily shows U.S. troops engaging forces from China or a united Middle East coalition. But in a modified video trailer posted on Islamic websites and shown to lawmakers, the game depicts a man in Arab headdress carrying an automatic weapon into combat with U.S. invaders.
"I was just a boy when the infidels came to my village in Blackhawk helicopters," a narrator's voice said as the screen flashed between images of street-level gunfights, explosions and helicopter assaults.
[Update: BoingBoing reports that the games described in the second article may be a hoax.]
Thursday, May 04, 2006
A first look at Sakai (an open-source competitor of WebCT and BlackBoard) - installing and running the Windows demo
Course management systems (e.g., WebCT, BlackBoard) are now ubiquitous on campuses across the country. These programs allow instructors to run courses online in a secure environment where they can post powerpoint slides, host quizzes, hold discussions, and do just about anything else they want with students. Students, on the other hand, have to log in to access the material (so it's not publicly accessible), and can see only what their instructor allows them to. All in all these systems are great educational tools that every college educator should use.
However, the two primary programs available (WebCT and BlackBoard) are commercial products that are extremely expensive (tens of thousands of dollars a year per campus). There are multiple open source alternatives (which are completely free to install and use): the two I know of are Sakai and Moodle. I'm currently using Moodle, and like it, but unfortunately my campus stopped actively supporting it more than a year ago, and I've now been told that the Moodle server is going away for good next fall. I'm extremely mad about this; Moodle is very similar to WebCT (see my comparison of the two for more information), and it's free. Our campus would easily save tens of thousands of dollars a year (if not more) by switching from WebCT to Moodle, but instead we're completely dropping Moodle (but I digress ... that's a topic for another post).
So, I need to find an alternative. My campus heavily supports WebCT, but I'm hesitant to move all of my online materials into a commercial, closed-source product. I've seen a lot of instructors have to waste hundreds of hours converting material from one commercial product to another; I don't want to ever have to do that myself. Also, I like supporting a free, open-source content management system, if only because if they were widely adopted they could easily save higher-education users hundreds of thousands (if not millions) of dollars a year.
While at the Innovations meeting (tag: Innovations), I attended a presentation about Sakai. The program looked very good, and appeared to be easy to use, so I wanted to give it a try. While Sakai is designed to be hosted on Unix servers, it advertises that it has a demo version that can run on Windows and is "perfect for a quick and easy demo of Sakai". I decided to try it out.
Installing the demo was anything by quick and easy.
[WARNING: Skip this paragraph if you don't like reading about bad instructions and problematic installations]. The demo download was a single zip file that I easily unzipped; it had no installation program that needed to be run. The demo_readme instructions said to run a batch file called "start-sakai.bat", which sounded easy enough. Unfortunately, the batch file returned an error that Java was not installed. I eventually found the file RUNNING.txt, which informed me that I needed to "Download and Install the J2SE Runtime Environment (JRE)" (J2SE). I did so, re-ran the batch file, and got another error (this time that JAVA_HOME wasn't set). This page had the solution; it turns out that I needed to manually set the JAVA_HOME variable. To do this I had to go into the system menu's advanced screen (Start -> Control Panel -> System -> Advanced -> Environment Variables) and manually add the variable. I did this, reran the batch file, and got another error. This one informed me that while I had JRE installed, I actually needed the Java SDK instead (and needed to set the variable JAVA_HOME to point to the SDK directory). So, I downloaded the Java SDK, installed it, and re-set the JAVA_HOME variable (which was to the directory "C:\program files\Java\jdk1.5.0 06"; not the one Sakai specified). I finally was able to run the batch file without error, though it did pop up a Tomcat window that quickly filled with dozens of meaningless messages before finally saying "server startup in 361520 ms" (that's 6 minutes). The Tomcat window never bothered to notify me that the server was running - I eventually just went to the URL included in the readme (http://localhost:8080/portal) and it worked.
So, to help others run this demo, here are some (hopefully clearer) installation instructions:
Sakai is an extremely flexible course management system - it can easily host multiple sites (courses) on a single installation, allow access to those sites from thousands of users, and each site can add and remove countless tools. It is probably more similar (in appearance) to WebCT than Moodle is, which might appeal to some users.
Keep in mind that by running this demo you're seeing what the site administrator sees (and needs to see) to administer an entire campus's online courses; there's much more available than what an individual instructor needs to run a single course. As such, using this demo has a bit of a learning curve, and I'm still climbing that right now; I'll try to post more once I've had time to play and learn.
[Note: The online help within Sakai is very well written. At the very least I'd recommend reading the "Course/Project Sites" portion of the online help menu; the portion on "create/add/edit/delete work sites" has an excellent walkthrough on how to create a new course within Sakai. Reading it will save you hours of frustrated clicking as you try to figure out how to create a course.]
However, the two primary programs available (WebCT and BlackBoard) are commercial products that are extremely expensive (tens of thousands of dollars a year per campus). There are multiple open source alternatives (which are completely free to install and use): the two I know of are Sakai and Moodle. I'm currently using Moodle, and like it, but unfortunately my campus stopped actively supporting it more than a year ago, and I've now been told that the Moodle server is going away for good next fall. I'm extremely mad about this; Moodle is very similar to WebCT (see my comparison of the two for more information), and it's free. Our campus would easily save tens of thousands of dollars a year (if not more) by switching from WebCT to Moodle, but instead we're completely dropping Moodle (but I digress ... that's a topic for another post).
So, I need to find an alternative. My campus heavily supports WebCT, but I'm hesitant to move all of my online materials into a commercial, closed-source product. I've seen a lot of instructors have to waste hundreds of hours converting material from one commercial product to another; I don't want to ever have to do that myself. Also, I like supporting a free, open-source content management system, if only because if they were widely adopted they could easily save higher-education users hundreds of thousands (if not millions) of dollars a year.
While at the Innovations meeting (tag: Innovations), I attended a presentation about Sakai. The program looked very good, and appeared to be easy to use, so I wanted to give it a try. While Sakai is designed to be hosted on Unix servers, it advertises that it has a demo version that can run on Windows and is "perfect for a quick and easy demo of Sakai". I decided to try it out.
Installing the demo was anything by quick and easy.
[WARNING: Skip this paragraph if you don't like reading about bad instructions and problematic installations]. The demo download was a single zip file that I easily unzipped; it had no installation program that needed to be run. The demo_readme instructions said to run a batch file called "start-sakai.bat", which sounded easy enough. Unfortunately, the batch file returned an error that Java was not installed. I eventually found the file RUNNING.txt, which informed me that I needed to "Download and Install the J2SE Runtime Environment (JRE)" (J2SE). I did so, re-ran the batch file, and got another error (this time that JAVA_HOME wasn't set). This page had the solution; it turns out that I needed to manually set the JAVA_HOME variable. To do this I had to go into the system menu's advanced screen (Start -> Control Panel -> System -> Advanced -> Environment Variables) and manually add the variable. I did this, reran the batch file, and got another error. This one informed me that while I had JRE installed, I actually needed the Java SDK instead (and needed to set the variable JAVA_HOME to point to the SDK directory). So, I downloaded the Java SDK, installed it, and re-set the JAVA_HOME variable (which was to the directory "C:\program files\Java\jdk1.5.0 06"; not the one Sakai specified). I finally was able to run the batch file without error, though it did pop up a Tomcat window that quickly filled with dozens of meaningless messages before finally saying "server startup in 361520 ms" (that's 6 minutes). The Tomcat window never bothered to notify me that the server was running - I eventually just went to the URL included in the readme (http://localhost:8080/portal) and it worked.
So, to help others run this demo, here are some (hopefully clearer) installation instructions:
- Download the Sakai 2.1.2 demo zip file (from here) and unzip it (the directory that contains the files can go anywhere; I just put it on the desktop).
- Download Sun's J2SE 5.0 Java Software Developers Kit (called JDK 5.0). Navigate to the "Get Java SE page" from here (the download should be available from this page).
- Install JDK 5.0; selecting the defaults should be fine.
- Locate the directory where JDK 5.0 was installed (probably C:\program files\Java\jdk1.5.0 06, or something similar).
- Create an environment variable called JAVA_HOME that is set to the location where JDK 5.0 was installed. To do this open up the system menu from the control panel (Start -> Control Panel -> System), navigate to the "Advanced" tab, and click the "Environment Variables" button. In the user variables area of that menu click the "New" button, type "JAVA_HOME" in the "Variable Name" box, and put the directory where JDK 5.0 was installed (probably C:\program files\Java\jdk1.5.0 06) in the "Variable value" box. Click OK to get out of the system menu.
- Navigate to the directory you unzipped the Sakai demo to and double click on the "start-sakai.bat" file.
- Once the Tomcat window has opened and finished reporting its various messages, open a web browser and navigate to the page http://localhost:8080/portal (the Tomcat Window may not report that the server is running). If all has gone well, you should see a working Sakai installation.
- The default login is the administrator account (admin / admin), which lets you start creating course sites and modifying the configuration.
Sakai is an extremely flexible course management system - it can easily host multiple sites (courses) on a single installation, allow access to those sites from thousands of users, and each site can add and remove countless tools. It is probably more similar (in appearance) to WebCT than Moodle is, which might appeal to some users.
Keep in mind that by running this demo you're seeing what the site administrator sees (and needs to see) to administer an entire campus's online courses; there's much more available than what an individual instructor needs to run a single course. As such, using this demo has a bit of a learning curve, and I'm still climbing that right now; I'll try to post more once I've had time to play and learn.
[Note: The online help within Sakai is very well written. At the very least I'd recommend reading the "Course/Project Sites" portion of the online help menu; the portion on "create/add/edit/delete work sites" has an excellent walkthrough on how to create a new course within Sakai. Reading it will save you hours of frustrated clicking as you try to figure out how to create a course.]
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