Parasitic butterflies

Now this is cool - a journal article in Nature details the evolution of a lineage of parasitic butterflies in the genus Maculinea. If you didn't know that there were parasitic butterflies, you're probably not alone - I didn't know it before reading this paper, though there are apparently 80 species of parasitic or carnivorous lepidopterans (butterflies and moths).

Species in the Maculinea genus live across Europe and Asia, and their larvae parasitize ants:

Initially they [Maculinea caterpillars] feed on the flowers of specific Lamiaceae, Gentianaceae or Rosaceae host plants. When they reach the fourth instar, they drop to the ground and are picked up by Myrmica (or in a few cases Aphaenogaster) ants and carried into the nest where they feed as parasites. Most currently recognized species, including the widely distributed species M. arion, M. teleius and M. nausithous and the east Asian Maculinea arionides prey on ant brood [larvae]. In contrast, Maculinea alcon and Maculinea rebeli are ‘cuckoos’, whose larvae are fed primarily on regurgitations from ant workers, trophic eggs and prey items. [wikipedia links added by me]

The journal article goes on to describe the evolutionary relationships of the different species of Maculinea and a number of related genera of butterflies, including Phengaris and Glaucopsyche. Butterflies in the genus Glaucopsyche are ant mutualists that pupate in ant nests without harming the ants at any point. It appears likely that mutualist species (that pupated in ant nests) evolved first, followed by predatory species (that consumed ant larvae), while the cuckoo species (which do not consume the ants but instead trick the ants into feeding them) evolved last.

The full phylogeny of Maculinea is available online for free (as is a phylogeny of related genera); they're both great figures that illustrate the change from mutualist to predatory parasite to cuckoo-like parasite.

The abstract of the paper is available here, and the full paper is available here.

(Via Premenopaws )

Als, TD, R Vila, NP Kandul, DR Nash, S Yen, Y Hsu, AA Mignault, JJ Boomsma, and NE Pierce. 2004. The evolution of alternative parasitic life histories in large blue butterflies. Nature 432, 386-390.

Categories:

• biology
• research
• invertebrate
• insect

That prayer study is popular

My prayer post has been picked up by a lot of bloggers; as the various reactions and commenters' comments are interesting, I'll link to all of the posts linking back to me that I've found so far (if I've left anyone off the list please let me know):

• That prayer boondoggle - Pharyngula (69 comments)
• Prayer and medicine - Terry's LJ (10 comments)
• Healing and the Power of Prayer - toolkitzone blog (4 comments)
• Desantoos's two posts - (1 comment)
• The unnecessary hypothesis - Newton's Binomium (0 comments)
• Power of Prayer Study Results - Adirondack Musing (0 comments)
• Doctorfedora's post (0 comments)

The post was also picked up by a discussion board and even showed up in the "related blogs" portion of the New York Times article I cited.

And, as one might expect, the study result is quickly becoming fodder for jokes. This post, by a person suffering from a painful medical problem, elicited this response by a commenter:

Oh, I've been thinking about you, too! But emphatically no praying! I care too much!

Categories:

• science
• religion
• blogging

Collard greens with bacon and onions

On my recent trip to Atlanta, I got to enjoy some great food, including dinner at a southern tea room. The tea room had collard greens with bacon and onions on their menu; since my SO and I have made that dish a number of times, I had to try them to see if we were coming anything close to what the dish was "supposed" to be. I was pleasantly surprised to find that the two were nearly identical. So, yesterday we cooked up another batch of collard greens at home, and they're this week's end-of-the-week recipe blogging post.

Collard greens are somewhat bitter, but not unpleasantly so, and, well, leafy. Flavoring them with bacon, onions, and vinegar results in a savory, tangy, slightly bitter dish that goes very well with creamier foods (like mashed potatoes).

1/4 pound bacon
1 medium onion, coarsely chopped
2 cloves garlic, finely minced or pressed with a garlic press
2 pounds collard greens
1 teaspoon kosher salt
vinegar to taste (we use rice vinegar, though others would work)

1. Rinse the collard greens and cut out the thick central vein. Chop into 1-inch-wide strips.
2. Cut the bacon into chunks (~3/4-inch wide); this is easier to do if the bacon is at least partially frozen.
3. Cook the bacon in a large pot over medium heat, stirring frequently, until the bacon is lightly browned and the fat has mostly rendered out (at least 10 minutes, but likely more).
4. Add the onion, increase the heat to medium-high, and cook, stirring frequently, until the onions have started to brown (5-10 minutes).
5. Add the garlic and cook, stirring constantly, for another minute.
6. If your pot can't hold all the raw collard greens at once, add them in a few batches (they cook down quickly); otherwise, add them all at once. Cook, stirring, until the greens are all coated with bacon fat and have reduced in volume.
6. Add enough water to almost cover the greens, add the salt, and bring to a boil.
7. Reduce the heat and simmer, covered, until the collard greens are tender (~15 minutes; test them by tasting).
8. We like to serve the collard greens with some of the cooking liquid in each bowl; if you'd prefer drier greens, then boil off the cooking liquid before serving.
9. Serve with vinegar and salt to taste. Radagast likes to add about 1-2 teaspoons of vinegar to a bowlful; Radagast's SO sometimes doesn't even add vinegar. You can also try adding a bit of sugar.

Notes:

This dish can be made with mustard greens as well, though the cooking time might vary.

This recipe is based on one from Rombauer et al. 1997.

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

Categories:

• cooking
• recipe
• American
• sidedish

Rhosgobel's essential tags

The advantage of using tags to organize my posts is that I can use any word as a tag; there's no limit to how many tags I can create, or how many tags a single post can have. This flexibility allows for very fine-grained organization of my posts. However, this is also a disadvantage, as I could quickly create thousands of unique tags that do nothing to organize the content of the site. So, to try to keep my tags organized, I've created a list of key tags that I'll try to use regularly:

• science
• biology
  
• teaching - Experiences teaching at a community college, teaching tips, educational technology, etc.
• research - Posts about my own research, research techniques, or research papers
  
• politics
• cooking
  
• linux - All things relating to Linux and open-source software
• photo - Posts with my own photographs
• personal - Posts looking at the personal side of things, including personal updates (being sick, being busy, etc.)
• house - Posts related to our house: remodeling, gardening, cleaning, etc.
• fun - Humor, games, survey memes, etc.
• blogging - Posts that look at blogging itself
  

I'll use other tags when they're relevant (and those other tags will likely be useful for finding specific content), but the list above should serve as a basic framework for exploring my posts.

[The links above lead to my del.icio.us pages for each of the tags.]

Categories:

• tagging
• blogging
• del.icio.us

Tagging posts - the beginning

I've decided to use Johan Sundström's Blogger publish ping and categorizer tool, a Greasemokey script (download) that runs in Firefox, to add del.icio.us tags to all of my posts.

As I mentioned previously, Blogger lacks the ability to tag or categorize posts. So, this means that if a reader wanted to find all my posts on a given topic, they'd have to either read through my entire archive chronologically, or do searches on my blog. Neither of those is terribly user friendly; what would be easier is if while writing a post I could tag the post as belonging to a specific category (e.g., politics, Linux), and then provide links to pages that listed all posts tagged with that term.

Lots of people have created hacks (big list here) that attempt to add this functionality to Blogger. The two primary methods used are including keywords in posts that searches can locate, or using social-bookmarking sites (like del.icio.us) to add tags to posts. I've decided on the latter, primarily because it seems like the social-bookmarking sites have more flexibility for organizing posts once they're tagged (and, at the very least I'll have a nicely organized list of my posts in del.icio.us when I'm done).

In the past I've manually created a few category pages (cooking, Linux, community college jobs, etc.), but manually updating them is a pain. I've also tried manually adding tags to posts, but it has proven to be time consuming and difficult to keep up. The script I'm using (instructions on using the script can be found here and here) automates the entire process of tagging posts and creating category pages; it does the following:

• Adds a "tag" field to the Blogger post editor that allows me to enter custom tags for each post.
• Automatically formats the tags into appropriate HTML code that is CSS-style-sheet compatible.
• Creates a "ping Del.icio.us" link that allows me to register my posts with Del.icio.us without having to fill in any forms.
  

This is all possible thanks to greasemonkey. Greasemonkey is an extension for Firefox that allows users to run custom scripts (see userscripts.org) in their browser. So, when I say that the script adds a "tag" line to the post editor, what's actually happening is that the script detects that I'm loading up the Blogger post editor, and then re-writes the HTML of the post-editor page to show a "tag" field. Snazzy.

The primary downside of this method is that it relies on a script that runs on my computer; if I post from another machine that doesn't have the greasemonkey script installed, the post editor will be back to its default, tag-less state. Considering that I post from only a few machines, this shouldn't be too much of an issue for me.

The script automatically adds the tags to the post page in an HTML division, so the tag line can be formatted by editing the style portion of the post template. The script author has a walkthrough here, but he's using a different template than I am, so his edits didn't work for me. Here are the relevant portions of my revised template (this page on CSS styles of unordered lists was very useful):

.PostFooter{line-height:10px;margin-bottom:10px;margin-left:0px;color:gray;font-size:10px}
div.tags { margin: 0; padding: 0 0 0 0px; color:gray;font-size:10px; margin-top: 10px}
div.tags ul { list-style-type: none; padding-left: 0; margin-left: 0; display:inline; padding-bottom: 0; margin-bottom: 0}
div.tags li { padding-left:14px; margin-left:0px; background: url('http://del.icio.us/static/img/delicious.small.gif') no-repeat 0 3px; display:inline; text-transform:capitalize;}

I also had to remove a break from the end of my template's body section, as otherwise there was a lot of space between the tag list and post footer. (note: I'm a CSS novice, so use the code above at your own risk)

All of my new posts should now have tags that appear as links at the bottom of the post; clicking on the tags will take you to a del.icio.us page that lists all my posts that have the same tag. I hope to go back and tag all of my older posts, though that will take a while.

The other change I plan to make is to add constantly-updated category pages right here on Rhosgobel (so you don't have to go to del.icio.us to see all the posts in a category). To do this I plan to use either this technique or this technique, but it'll be a while before I get to working on those.

[For those curious about how this works, I've created an account for Rhosgobel on del.icio.us, and all posts I make will be bookmarked by that account. In addition to the standard tags, each post will also be tagged with "Rhosgobel" (my anchor tag). Thus, to find posts from this blog that are tagged with a given tag (let's say "cooking"), the link actually searches for all posts tagged with "Rhosgobel" and the given tag ("cooking") in the Rhosgobel account.]

Categories:

• tagging
• blogger
• blogging
• del.icio.us

Political news of the week, take 7

[See also: political links of the week take 6, take 5, take 4, take 3, take 2, and take 1.]

Bush Was Set on Path to War, British Memo Says - A New York Times article about a secret memo detailing conversations between Bush and Blair just before the start of the Iraq war.

In the weeks before the United States-led invasion of Iraq, as the United States and Britain pressed for a second United Nations resolution condemning Iraq, President Bush's public ultimatum to Saddam Hussein was blunt: Disarm or face war.

But behind closed doors, the president was certain that war was inevitable. During a private two-hour meeting in the Oval Office on Jan. 31, 2003, he made clear to Prime Minister Tony Blair of Britain that he was determined to invade Iraq without the second resolution, or even if international arms inspectors failed to find unconventional weapons, said a confidential memo about the meeting written by Mr. Blair's top foreign policy adviser and reviewed by The New York Times.

...

The memo indicates the two leaders envisioned a quick victory and a transition to a new Iraqi government that would be complicated, but manageable. Mr. Bush predicted that it was "unlikely there would be internecine warfare between the different religious and ethnic groups." Mr. Blair agreed with that assessment.

The memo also shows that the president and the prime minister acknowledged that no unconventional weapons had been found inside Iraq. Faced with the possibility of not finding any before the planned invasion, Mr. Bush talked about several ways to provoke a confrontation, including a proposal to paint a United States surveillance plane in the colors of the United Nations in hopes of drawing fire, or assassinating Mr. Hussein.

Bush Has No Plans to End War:

During yesterday's press conference, President Bush was asked when the troops could come home from Iraq and he answered, "that will be decided by future presidents and future governments of Iraq." It is clear that he has no intention of finding an end to this conflict and it will take a new administration in 2009 to bring the troops home.

Lobbysist Abramoff, pal Kidan get 5 years, 10 months each in SunCruz fraud case:

Disgraced former lobbyist Jack Abramoff was sentenced Wednesday to five years, 10 months in prison by a federal judge for his role in a fraud scheme with a former partner during their purchase in 2000 of the SunCruz Casinos gambling fleet.

Abramoff, 47, and ex-partner Adam Kidan, 41, received the same sentence, the minimum under federal guidelines.

Call to Censure Bush Is Answered by a Mostly Empty Echo - A New York Times article about this week's hearing on Feingold's censure motion.

Five Republicans at the hearing took turns attacking the idea as a reckless stunt that could embolden terrorists. Just two Democrats showed up to defend it, arguing that Congress needed to rein in the White House's expansive view of presidential power.

...

Senator Patrick J. Leahy of Vermont, the ranking Democrat on the committee and the only other Democrat to speak at the hearing [other than Feingold], said he, too, was inclined to support censure. Only two other senators, Tom Harkin of Iowa and Barbara Boxer of California, have signed on as co-sponsors of Mr. Feingold's resolution.

Republicans argued that censure would undermine the president's efforts to fight terrorism.

"This hearing, I think, is beyond the pale," said Senator John Cornyn, Republican of Texas.

Mr. Cornyn argued that the censure proposal could send a "perverse and false message" of presidential weakness to terrorists around the world and thus "make the jobs of our soldiers and diplomats harder and place them at greater risk."

Baghdad? Suburb of Istanbul? Same thing ... - A post of my own looking at a Republican Congressional candidate using a photo of a city in Turkey to demonstrate how peaceful Baghdad is.

Schools Cut Back Subjects to Push Reading and Math - A New York Times article looking at the effect that No Child Left Behind is having on education (via Orac):

Schools from Vermont to California are increasing — in some cases tripling — the class time that low-proficiency students spend on reading and math, mainly because the federal law, signed in 2002, requires annual exams only in those subjects and punishes schools that fall short of rising benchmarks.

The changes appear to principally affect schools and students who test below grade level.

The intense focus on the two basic skills is a sea change in American instructional practice, with many schools that once offered rich curriculums now systematically trimming courses like social studies, science and art. A nationwide survey by a nonpartisan group that is to be made public on March 28 indicates that the practice, known as narrowing the curriculum, has become standard procedure in many communities.

The survey, by the Center on Education Policy, found that since the passage of the federal law, 71 percent of the nation's 15,000 school districts had reduced the hours of instructional time spent on history, music and other subjects to open up more time for reading and math ...

The First Step in Increasing the NIH Budget - Orac and Evolgen have both been tracking the proposed NIH research budget (which was is going to be cut), and have some good news about a senate amendment that increases the research budget [update: see the next entry for the latest on this topic]:

The Specter-Harkin Amendment passed the Senate, but this does not guarantee an increase to the NIH budged. The House must still vote on it and it must be reflected in House and Senate Appropriations Committees' allocation for the Labor-Health and Human Services Appropriations Committee. ...

That said, an important step has been taken towards ensuring important biomedical research gets funded. The amendment passed by a vote of 73 to 27. [Evolgen includes a list of senators voting for and against the amendment in the original post].

One more chance to support the NIH - After reporting the good news (above) a few days ago, today Orac reported that the NIH budget is once again in trouble; Orac's post has a list of ways you can help in the coming week.

Evolgen previously reported on the success of the Specter-Harkin Amendment in the Senate to change a completely flat National Institutes of Health (NIH) budget containing actual real cuts to the budget of the National Cancer Institute (NCI) to one with a modest increase in fiscal year 2007. Both the American Association of Cancer Research (AACR) and Genetics Society of America both weighed in when the budget was sent to the House in order to garner support in committee for adding an amendment similar to the Specter-Harkin Amendment to the Department of Health and Human Services budget.

Apparently, the effort to add this amendment to the HHS budget has failed, with the House Budget Committee electing to go with a version of the HHS budget that resembles the President's meager budget.

How Environmentalists Lost the Battle Over TCE: The first of a two part LA Times series looking at how the Pentagon successfully prevented the EPA from creating more stringent regulations surrounding a potential carcinogen that is contaminating water supplies:

Following four years of study, senior EPA scientists came to an alarming conclusion: The solvent, trichloroethylene, or TCE, was as much as 40 times more likely to cause cancer than the EPA had previously believed.

The preliminary report in 2001 laid the groundwork for tough new standards to limit public exposure to TCE. Instead of triggering any action, however, the assessment set off a high-stakes battle between the EPA and Defense Department, which had more than 1,000 military properties nationwide polluted with TCE.

By 2003, after a prolonged challenge orchestrated by the Pentagon, the EPA lost control of the issue and its TCE assessment was cast aside. As a result, any conclusion about whether millions of Americans were being contaminated by TCE was delayed indefinitely.

President Straw Man - Orac reports on an AP article discussing the use of straw-man arguments by politicians (and then, a day later, Orac noticed some more; one could make a career of pointing out straw man arguments by politicians).

[A] straw man argument is the refutation of a weaker argument than the one that one's opponent has actually proposed. Most commonly, it involves either paraphrasing one's opponent's argument in highly weakened form or misrepresenting it completely in such a way that it is more radical or less nuanced, attributing that weaker argument to him or her, and then refuting that argument. The weaker argument is the "straw man" that is knocked down in place of one's opponent's true argument. The use of the straw man argument can represent either dishonesty or merely sloppy thinking (or a combination of the two), and it is one of the most common logical fallacies I (and most others interested in skepticism and critical thinking) encounter.

Science teachers in Arkansas self-censoring about evolution:

Via Red State Rabble, I've become aware of an incredibly depressing story about science teachers in Arkansas explicitly censoring themselves when it comes to teaching evolution (the "e-word," as they call it) or in geology class teaching that the earth is 4.5 billion years old:

...

The teachers there are so frightened of the reaction of fundamentalists that they wouldn't allow the reporter to mention the name of the school, nor would the teachers cooperate without assurances of anonymity

Gov., Rivals Leave Fiscal Crisis in the Wings - And, to end with some California politics, the LA Times reports that none of the gubernatorial candidates (yes, there is going to be another big California election this November) are addressing the impending financial problems of the state.

The cash crunch — the state expects tax collections to fall at least $5 billion short of its spending within three years — is apt to be one of the toughest challenges facing the next governor. It threatens to undercut schools, hospitals, transportation and other public services even as the state's population, and its needs, keep growing.

Yet Schwarzenegger and one of his Democratic opponents, Controller Steve Westly, have offered no concrete plans to close the budget gap. Neither has identified any spending he would cut if elected in November, and both have said higher taxes would be only a last resort.

...

While keeping his future budget plans vague, Schwarzenegger has been bold about how he defines his fiscal record so far: He takes credit for saving the state from bankruptcy. He argues that by cutting the cost of insurance for workplace injuries, slashing the car tax and refusing to raise income taxes, he has created a business climate that spawned 500,000 jobs on his watch, along with a surge in new tax revenue.

...

The state's job growth has occurred in sync with the rest of the country's. And Thornberg, the UCLA economist, said Schwarzenegger's policies had nothing to do with the surge in tax collections.

"The fact is, Schwarzenegger is no more responsible for the recovery the state's economy is going through than Gray Davis was responsible for the collapse of the tech sector," he said. The dot-com bust wiped out billions of dollars in tax revenue while Davis was governor.

It is largely the surge of unexpected tax revenue, along with billions of dollars in new borrowing under Schwarzenegger, that has pulled California out of the fiscal crisis.

The governor has restrained spending substantially in just one area, slowing the legally mandated growth of the education budget.

Categories:

• politics
• news
• Bush
• teaching
• research

Testing tags

This is a test post to explore methods for organizing my posts. More details to come in a later post.

Categories:

• tagging
• blogger
• blogging

Why I love living in Southern California

While people like PZ freeze, my yard is filled with these:



This is an English Garden David Austin English rose.

English roses are by far my favorite type of rose - they have gorgeous, complex blooms and are bred to smell incredibly good; if you've never smelled a Prince rose on a warm, sunny day, you've never really smelled a rose. And, thanks to living in Southern California, I have half a dozen Prince blooms sitting on my dining room table right now.

Categories:

• photo
• rose
• house
• California

Prayer doesn't heal

A New York Times article started off with a sentence that should come as no surprise to most skeptical thinkers:

"Prayers offered by strangers had no effect on the recovery of people who were undergoing heart surgery, a large and long-awaited study has found."

The study under discussion (Benson et al. 2006) is a multi-year, multi-thousand participant study that examined the effect of prayer on patients undergoing heart surgery. The study treats its subject matter with deadly seriousness; I'm not a medical doctor, but from what I can tell the methods in the study were clean, precise, and exactly what I'd look for in any study of a possible medical treatment.

The study included patients who were undergoing coronary artery bypass graft (CABG) surgery. The study's coordinators asked more than 3,000 patients at six different hospitals in the United States to participate, and they ended up with more than 1,800 patients in the study. The patients were randomly divided into three groups:

• Patients who were prayed for, but were told that they "may or may not be prayed for." (Group 1)
• Patients who were not prayed for, but were told that they "may or may not be prayed for." (Group 2)
• Patients who were prayed for, and were told that they "will be prayed for." (Group 3)
  

Those patients who were prayed for had their names sent to three different congregations (two Catholic and one Protestant), where congregants were instructed to pray for the patients for 14 days.

The study's methodology had a number of good points:

• Patients were randomly assigned to each treatment group.
• Patients were informed of their treatment group via a sealed letter; hospital staff were not informed of the patient's treatment group, and patients were told not to inform hospital staff of their assigned treatment.
• Data collection and analysis were conducted without knowledge of the treatment group of the patients.
• The treatment groups were sized to be able to statistically detect 10% changes in outcomes between the groups.
• The authors collected a tremendous amount of data about all participants (e.g., age, religion, cardiovascular history statistics, operation time) and showed that "[t]here were no important differences in baseline or operative characteristics across the 3 groups."
• Standard statistical analyses were used to analyze all the data.
  
• The statistical comparisons to be made appear to have been decided before the study commenced (a procedure that prevents data fishing).

The outcome the study authors examined was the number of complications each patient exhibited within 30 days of the surgery. The authors analyzed their data by doing two pairwise comparisons:

• Comparing the two groups (1 and 2) who were informed they might be prayed for; this tested whether prayer had any effect, since one group was prayed for and one group was not prayed for.
• Comparing the two groups (1 and 3) who were prayed for; this tested whether patient knowledge of prayer had any effect, since one group was certain they'd be prayed for while the other group was not certain.
  

A modified version of Benson et al.'s (2006) figure 2; their statistical analyses (chi-square tests) are summarized in the figure. The black bars at the top of each bar represent the number of patients who either did not undergo surgery or did not complete the study. [Axis labels were redrawn by me for clarity; everything else is original.]

Here's a quick summary of the results:

• Prayer had no significant effect on the number of patients experiencing complications after surgery (comparing groups 1 and 2, 52% vs. 51% of patients respectively; P=0.67). In other words, prayer did nothing.
  
• Patients who knew they were being prayed for had significantly more complications after surgery than patients who were prayed for but weren't sure they were being prayed for (comparing groups 1 and 3, 52% vs. 59% of patients respectively; P=0.025). In other words, knowing you were being prayed for appeared to hurt, not help.

Considering that there's no scientific evidence supporting the existence of a higher power in the first place, the first result is not unexpected. The second result is more interesting; it appears that knowing you are being prayed for actually makes you more likely to have complications post-surgery. This is probably not what religious backers of the study were hoping to find.

The authors did more data analysis than what is summarized above, but everything else follows the same trends identified above.

I am impressed by these authors - they appear to have done a first-class study on a very controversial topic. However, what's distressing is that the study will probably not change anyone's opinion. Those who already believe that prayer is useless didn't need a $2.4 million study to show as much, and those who believe in prayer will probably just rationalize this study away. Examples of this rationalization can be already found in many of the newspaper articles covering this study:

• "Working in a large medical center like Mayo, Mr. Marek [a hospital chaplain] said, 'You hear tons of stories about the power of prayer, and I don't doubt them.'" (NY Times)
• "A person of faith would say that this study is interesting," Mr. Barth [spiritual director of Silent Unity] said, "but we've been praying a long time and we've seen prayer work, we know it works, and the research on prayer and spirituality is just getting started." (NY Times)
• "Dr. David Stevens, executive director of the Christian Medical and Dental Associations, said he believes intercessory prayer can influence medical outcomes, but that science is not equipped to explore it. 'Do we control God through prayer? Theologians would say absolutely not. God decides sometimes to intervene, and sometimes not,' he said." (Houston Chronicle)
• "'Maybe the people weren't praying very hard,' Higgins said of the study. 'I have no doubts that intercessory prayer works, (just) not all the time.' Even Christ's prayers in the garden of Gethsemane weren't answered, Higgins said. 'At the end, it's God's will be done. ... I don't know how you can measure those things.'" (St. Petersburg Times)
  

It'd be nice if they had some data to back up their claims.

If there were a good rational basis for why prayer should work (and/or multiple other well-controlled studies showing that prayer did actually help), I could see listening to these critics and attempting to argue that maybe this study wasn't quite perfect and thus we should do more study. However, there is no good evidence that prayer does anything, and not even an evidence-supported mechanism for why prayer should work, so let's just call it a day and focus on remedies that might actually help people.

So, can prayer now be considered an altie treatment?


H Benson, Dusek JA, Sherwood JB, Lam P, Bethea CF, Carpenter W, Levitsky S, Hill PC, Clem DW, Jain MK, Drumel D, Kopecky SL, Mueller PS, Marek D, Rollins S, and Hibberd PL. 2006. Study of the Therapeutic Effects of Intercessory Prayer (STEP) in cardiac bypass patients: A multicenter randomized trial of uncertainty and certainty of receiving intercessory prayer. American Heart Journal 151 (4): 934-942 (abstract)

Thanks to PZ Myers for helping locate the original journal article.

Categories:

• science
• research
• prayer
• religion

Organizing my posts

One of the biggest downsides of using Blogger is that there is no built-in method to organize posts by topic. Just about every other blogging platform (e.g., WordPress, MoveableType) supports this feature, and most other bloggers use categories prolifically (e.g., Pharyngula, Respectful Insolence, Semantic Compositions). Since I write on such a diverse array of topics, I imagine that readers would prefer to read posts on whatever single topic (e.g., cooking, Linux, politics, science) interests them, rather than having to wade through all my posts in chronological order.

So, I'm now hunting for a mechanism to organize my posts. As part of a giant list of Blogger hacks, Freshblog has a two post series that discusses three different methods for adding del.icio.us or technorati tags to posts. Rahul Gupta also has a walkthrough on tagging, complete with links to other blogs that have done the same. There's even FreshTags, a site that has code that allows users to navigate tagged posts via the sidebar (though the navigation interface isn't quite as intuitive as many category implementations are).

There are also multiple methods to create categories: netcf2 has a script that uses Blogger Search to create categories, and there's also an independent service, lablr, that is designed to integrate with Blogger templates to add categories. Sambot compares tags and categories, and argues that tags are better than categories; in doing so Sambot summarizes the benefits of each technique.

In the coming days I'll likely be exploring various options for organizing my posts. If anyone has suggestions on how to best implement tags or categories here on Blogger, or has preferences for tags or categories they'd like to see here, I'm all ears!

[Update: I've decided to tag my posts with del.icio.us; I've written more about this here and here.]

Categories:

• blogger
• blogging
• tagging

Coalition war deaths in Iraq

BoingBoing linked to an animation showing the number of troop deaths on each day of the war in Iraq. Here's the author's description:

The animation runs at ten frames per second - one frame for each day [of the war in Iraq] - and a single black dot indicates the geographic location that a coalition military fatality occurred. Each dot starts as a white flash and a larger red dot which fades to black over the span of 30 frames/days, and then slowly fades to grey over the span of the entire war.

Accompanying the visual representation is a soft 'tic' sound for each fatality, the volume of which increases relative to the number of fatalities that occurred simultaneously that day. More deaths in a smaller area produces visually deeper reds and audibly more pronounced 'tic's.

This goes well with the Washington Post's Faces of the Fallen project.

Categories:

• politics
• Iraq

Catching up on the posts ...

Sheesh, I ignore the blogosphere for a week and a whole bunch of great posts get written:

Confessions of a Community College Dean looks at how community colleges are portrayed in Strapped, a book by Tamara Draut; in doing so the Dean counters some common misconceptions about the role of community colleges in higher education.

PZ Myers wrote an excellent post on the molecular underpinnings of fly eye development.

Deep Sea News summarized the variety of habitat types found in the deep ocean.

Prometheus analyzed how some mail-order labs bias their tests so that they are much more likely to report an abnormally high level of some toxic compound (e.g., urine mercury concentration, which is often used to support alternative-medicine claims that mercury poisoning is causing autism). (Via Orac)

Orac started a new series on his blog called Medicine and Evolution, and as the series' inaugural post he summarized a study that uses an ecological diversity index to predict the likelihood that a non-cancerous condition (Barrett's esophagus) will develop into cancer. Very neat stuff.

UBC Botany Photo of the Day had a picture of Illicium anisatum (Japanese star anise), which is toxic, even though it's a close relative of Illicium verum (the star anise commonly used in cooking). According to the Wikipedia, the two are sometimes confused, leading to unhappy consequences.

And, for a bit of fun, Orac linked to an amazing lego aircraft carrier.

Categories:

• biology
• science
• blogging
• fun

Baghdad? Suburb of Istanbul? Same thing ...

Howard Kaloogian, a Republican candidate for California's 50th Congressional district (and chairman of the Recall Gray Davis Committee), posted the following picture and accompanying text on his "Support Our Troops & The War Against Terrorism" issues page (Google cache):

Downtown Baghdad: We took this photo of dowtown Baghdad while we were in Iraq. Iraq (including Baghdad) is much more calm and stable than what many people believe it to be. But, each day the news media finds any violence occurring in the country and screams and shouts about it - in part because many journalists are opposed to the U.S. effort to fight terrorism.

There's only one problem: posters on DailyKos have determined that the picture was actually taken in Bakirkoy, a suburb of Istanbul, Turkey. Here's a picture of the same neighborhood taken by Faruk and posted on the wowTurkey.com website:


Photograph of Bakirkoy, Turkey, by Faruk on wowTurkey.com.

(Want more examples of politicians misusing images? Go take a look at a Bret Schundler campaign photo and Bush's plagiarized yakuza ad.)

[Update 7pm: Kaloogian's website has been updated; the picture has been replaced and the caption now reads: "We originally posted a photograph not of Baghdad, Iraq but from Istanbul, Turkey where our delegation traveled on the way home to the United States. We apologize for this mistake. We have corrected it with a photograph we took from Baghdad. We took this photo of downtown Baghdad ..."]

Categories:

• politics
• Iraq
• California

Banaras-style Pilaf

Now that it's spring break, my SO and I finally have time to cook again. Last night we made our yogurt braised chicken and served it with a pilaf and some spinach raita. The pilaf went extremely well with the chicken dish; the rice was very light and fluffy, and was flavored with cloves, cinnamon, and black cardamon (which has a smokier flavor than green cardamom). This pilaf was relatively easy to make and well worth the effort; if you're going to serve an Indian dish with rice, I'd highly recommend serving it with a pilaf (such as this one) instead of plain rice. This pilaf is this week's end-of-the-week recipe blogging post.

If all you've ever eaten are American-style pilafs ("I cooked my rice with chicken stock; now it's a pilaf"), you're in for a pleasantly flavorful surprise.

2 cups basmati rice
4 cups water
3 tablespoons vegetable oil
24 whole peppercorns
10 whole cloves (or 1/3 teaspoon ground cloves; add ground cloves with the ginger)
4 black cardamom pods (or 8 green cardamom pods)
1 bay leaf
1 3" cinnamon stick
2 teaspoons Kosher salt
2 teaspoons fresh ginger, peeled and finely chopped or grated

1. Rinse the basmati rice repeatedly with water in a large bowl until the water draining off is mostly clear.
2. Drain as much of the rinsing water from the rice as you can, and then add 4 cups of fresh water. Let soak for 30 minutes.
3. Drain the rice, reserving the soaking water (it will be used to cook the rice later).
4. Heat the oil in a nonstick pot over medium-high heat. When the oil is hot, add all the whole spices (peppercorns, cloves, cardamom pods, bay leaf, and cinnamon stick) and cook, stirring constantly, until they start to brown (~1-2 minutes)
5. Add the rice, and cook, stirring constantly, until the rice turns translucent (~5 minutes; Sahni states the rice should begin to brown, but it never does for us).
6. Add the water, salt, ground cloves (if using), and ginger. Bring to a boil, then turn down the heat and simmer, partially covered, for 10 minutes. At the end of this time the water should be mostly absorbed.
7. Turn the heat to the lowest setting possible, raise the pot above the burner (we set it on a wire roasting rack placed over the burner), and let sit, covered, for 10 minutes.
8. Turn off the heat and let sit for 5 minutes.
9. Fluff the rice with a fork, and serve.

Note:

You can leave the whole spices in the dish when you serve it, but should probably avoid eating them. This recipe is from Sahni (1980).

Sahni, Julie. 1980. Classic Indian Cooking. William Morrow & Co, NY. pp. 368-369.

Categories:

• cooking
• recipe
• pilaf
• Indian

Gack!

I finally got the courage to open up my feed reader (after a week of ignoring it), and found that I have 200-some posts to read. Luckily I'm on spring break this coming week, so I'll be able to curl up in my cozy computer chair and catch up.

Categories:

• blogging
• personal
• fun

Political links of the week, take 6

[See also: political links of the week take 5, take 4, take 3, take 2, and take 1.]

Once Protected by Hussein, Palestinians Suffer Backlash - an article in the New York Times about hate crimes against Palestinians in Iraq:

The bill of death appeared overnight on Thursday, addressed to "the Palestinian traitors," and the killers were specific in their intent.

"We warn you that we will eliminate you all if you don't leave the area for good within 10 days," the leaflet said. It was signed by a group calling itself the Judgment Day Battalion, and it was scattered in front of the homes of Palestinians in Al Hurriya, a northern Baghdad neighborhood.

Bound, Blindfolded and Dead: The Face of Atrocity in Baghdad - Another article in the New York Times about the current state of Iraq:

Mohannad al-Azawi had just finished sprinkling food in his bird cages at his pet shop in south Baghdad, when three carloads of gunmen pulled up.

In front of a crowd, he was grabbed by his shirt and driven off.

Mr. Azawi was among the few Sunni Arabs on the block, and, according to witnesses, when a Shiite friend tried to intervene, a gunman stuck a pistol to his head and said, "You want us to blow your brains out, too?"

Mr. Azawi's body was found the next morning at a sewage treatment plant. A slight man who raised nightingales, he had been hogtied, drilled with power tools and shot.

In the last month, hundreds of men have been kidnapped, tortured and executed in Baghdad. As Iraqi and American leaders struggle to avert a civil war, the bodies keep piling up. The city's homicide rate has tripled from 11 to 33 a day, military officials said.

...

What frightens Iraqis most about these gangland-style killings is the impunity. According to reports filed by family members and more than a dozen interviews, many men were taken in daylight, in public, with witnesses all around. Few cases, if any, have been investigated.

Bush shuns Patriot Act requirement:

When President Bush signed the reauthorization of the USA Patriot Act this month, he included an addendum saying that he did not feel obliged to obey requirements that he inform Congress about how the FBI was using the act's expanded police powers.

...

Bush signed the bill with fanfare at a White House ceremony March 9, calling it ''a piece of legislation that's vital to win the war on terror and to protect the American people." But after the reporters and guests had left, the White House quietly issued a ''signing statement," an official document in which a president lays out his interpretation of a new law.

In the statement, Bush said that he did not consider himself bound to tell Congress how the Patriot Act powers were being used and that, despite the law's requirements, he could withhold the information if he decided that disclosure would ''impair foreign relations, national security, the deliberative process of the executive, or the performance of the executive's constitutional duties.

Memos Reveal War Crimes Warnings:

The White House's top lawyer warned more than two years ago that U.S. officials could be prosecuted for "war crimes" as a result of new and unorthodox measures used by the Bush administration in the war on terrorism, according to an internal White House memo and interviews with participants in the debate over the issue.

The concern about possible future prosecution for war crimes—and that it might even apply to Bush adminstration officials themselves— is contained in a crucial portion of an internal January 25, 2002, memo by White House counsel Alberto Gonzales obtained by NEWSWEEK. It urges President George Bush declare the war in Afghanistan, including the detention of Taliban and Al Qaeda fighters, exempt from the provisions of the Geneva Convention.

In the memo, the White House lawyer focused on a little known 1996 law passed by Congress, known as the War Crimes Act, that banned any Americans from committing war crimes—defined in part as "grave breaches" of the Geneva Conventions. Noting that the law applies to "U.S. officials" and that punishments for violators "include the death penalty," Gonzales told Bush that "it was difficult to predict with confidence" how Justice Department prosecutors might apply the law in the future. This was especially the case given that some of the language in the Geneva Conventions—such as that outlawing "outrages upon personal dignity" and "inhuman treatment" of prisoners—was "undefined."

Senate hearing set on move to censure Bush - Senator Feingold's resolution to censure President Bush will be the subject of a hearing next Friday in the Senate Judiciary committee.

500,000 protest immigrant legislation:

In a mobilization that far exceeded the expectations of organizers, hundreds of thousands of people rallied in downtown Los Angeles on Saturday to protest legislation in Congress that would tighten enforcement against undocumented immigrants and erect more walls along the southern border.

...

The proposal that inspired the protests already has passed in the House of Representatives and is expected to be debated by the Senate this week. It includes strict measures that would make it a felony for immigrants to be in the United States without proper documentation, and it imposes criminal penalties on those who employ illegal immigrants. It would also finance the construction of tall fences along roughly one-third of the U.S.-Mexican border to try to stop illegal crossings.

Online sexual material is obscene if any community in US objects:

The Supreme Court of the United States has declined to overturn an important case about obscenity and the Internet, leaving anyone who publishes sexual material on the Internet in uncertainty about whether they're open to federal penalties.

At stake is the obscenity section of the Communications Decency Act, which bans publishing "obscene" material on the net. The problem is that US courts use "local standards" to determine whether something is obscene -- so if in the eyes of some local community, the material is obscene, then you can't distribute it there.

...

By turning down this case, the Supremes have said that the whole country is now subject to the decency standards from its most conservative, anti-sex, anti-nudity corners; that the local standard from that place will become the national standard.

Categories:

• politics
• news
• Iraq
• Bush

Mammal

[I'm exhausted, so here's a post from my draft files.]

I've loved They Might Be Giants from the moment a college friend and I went to a concert of theirs and got to stand in the front row about 6' away from the band. Thus I was happy to find that they have a song all about mammals (titled, appropriately enough, "Mammal"):

Glass of milk
Standing in between extinction in the cold
and explosive radiating growth
So the warm blood flows
Through the large four-chambered heart
Maintaining the very high metabolism rate they have

Mammal, mammal
Their names are called
They raise a paw
The bat, the cat
Dolphin and dog
Koala bear and hog

One of us might lose his hair
But you're reminded that it once was there
From the embryonic whale to the monkey with no tail
So the warm blood flows
With the red blood cells lacking nuclei
Through the large four-chambered heart
Maintaining the very high metabolism rate they have

Mammal, mammal
Their names are called
They raise a paw
The bat, the cat
Dolphin and dog
Koala bear and hog

Placental the sister of her brother Marsupial
Their cousin called Monotreme
Dead uncle Allotheria

Mammal, mammal
Their names are called
They raise a paw
The bat, the cat
Dolphin and dog
Koala bear and hog
The fox, the ox
Giraffe and shrew
Echidna, caribou

Even if you haven't gotten to go to one of their concerts, how could you not love a band that sings about the high metabolic rates of endotherms?

Categories:

• biology
• music

I'm back!

I'm back from Innovations; I'm feeling very innovative, and have more to post about the meeting, but unfortunately have no time right now. I'm exhausted from many 15-hour days of meetings and socializing, and have a lecture to give tomorrow that I've barely prepped for.

To entertain yourselves, go enjoy this real-life version of The Simpsons' opening.

Categories:

• teaching
• conference
• Innovations
• 2006
• personal
• fun

Innovations report - federal aid to Louisiana community colleges

Today was filled with excellent talks, great people, and good food. I love this meeting. It's amazingly motivating to be here surrounded by people who love teaching; I learned at least something in every session I attended.

Today's most interesting session was the keynote address by Dr. Walter Bumphus, president of the Louisiana Community and Technical College System. This year's meeting was in fact supposed to be held in New Orleans, but due to hurricane Katrina it was moved to Atlanta.

Dr. Bumphus's excellent lecture focused on how the community college system of Louisiana was affected by the hurricane, and detailed how they've responded to the challenges of rebuilding the affected colleges; it's a massive undertaking. The talk was recorded, so if you get a chance to see it, I'd recommend watching.

Probably the most memorable statement of the entire day was Dr. Bumphus's blunt summary of how much money the federal government has delivered to his system to aid in recovery efforts:

"We've gotten more money from student government associations than we've gotten from the federal government."

Shortly later he clarified that while they have received promises of funding,

"To date we've not received one federal penny."

Stunning.

[Note: I wrote the quotes down during the meeting as quickly as I could, but they may not be precisely accurate.]

Categories:

• teaching
• conference
• Innovations
• 2006
• Katrina
• politics

Innovations report - how to lobby the legislature

The first presentation I went to (and woke up early for) on Sunday was on creating electronic portfolios; it was, in fact, the only talk scheduled for 9:15am. The room was filled to capacity, except for one seat: the presenter's. It turns out that none of the people who showed up had noticed a tiny line item in the schedule errata that said the talk had been rescheduled. Oh well.

The first real talk I went to was much more interesting; it was presented by Dr. Joseph Opatz, president of Central Lakes College in Minnesota. Prior to being college president, Dr. Opatz served for more than a decade in the state legislature in Minnesota, so he has an interesting perspective on academic politics. Dr. Opatz presented his talk ("Lobbying your legislature: Making your college's case at the capitol") as a practical guide on how community college administrators can (and should) interact with their state legislators so as to benefit their colleges. While he only has experience with Minnesota politics, his ideas almost certainly transfer to most other states.

Dr. Opatz started the talk with a "how much do you know about lobbying" quiz. I failed miserably:

1. Name your state legislators, especially the ones that have your college in their district.
2. What are some personal details about your legislators (e.g., family details, careers, personal interests)?
3. What are the key features of your legislators' districts (especially the political leaning of the district)?
4. Name the committees your legislators serve on.
5. List the key policy interests of your legislators.
6. Name all the legislators that are college alumni, or whose spouses (or children) are students or alumni.
7. Name the legislators that sit on higher education committees (and, if possible, list how many of their district members attend your school).
   

The point of the quiz was not to illustrate how little the audience knew, but rather to illustrate that knowing the answers to all these questions can help you understand and interact with your elected representatives.

The primary suggestion Dr. Opatz had was to build personal relationships with the legislators that serve your district. Once you've built a relationship, your legislators will at least be familiar with you (and your institution) when bills or other items come up that need attention, and thus they'll be more likely to understand your specific needs and interests.

Obviously Dr. Opatz was not suggesting that college presidents and employees should become best friends with their representatives, but instead they should at least visit them and build professional relationships with them. Simple things like inviting your representatives to campus events, publicly thanking your representatives for their service when you see them attending college events, and visiting the capitol to meet them would all help. However, he also cautioned that you must remember that the legislator is probably exceptionally busy (he mentioned that the Minnesota legislature annually introduces about 3,000 bills), and thus you should never abuse the time you're given.

The presentation was packed with helpful information, and I'm sad to report that Dr. Opatz's slides are not available online. However, here's a short list of some of his suggestions that I was able to write down (keep in mind that this is my interpretation of his talk; Dr. Opatz has clearly not read this post):

• If you do get invited to testify at a committee: talk only for your allotted time, talk with the committee staff beforehand to see what they want you to talk about, and know exactly what you want before you go in (as you may be asked to give feedback on wording changes on the spot).
• If you do visit the capitol, have an "elevator speech" ready about your topic. In one minute you should be able to clearly state your problem, 1-3 facts backing up the problem (ideally with real life stories), and then propose your solution.
• When referring to bills, don't use just the bill number; it's likely that nobody will know what you're talking about.
• Remember to visit the capitol and talk to your legislator even when you don't have any important issues on the table. He reported that he regularly noticed which college presidents attended the higher education committee meetings. He also said that while most education lobbyists are treated as "just another lobbyist", personal visits from students, faculty, and administrators are often given more attention.
• Find opportunities for informal socializing, like inviting the representative to lunch or dinner; he said this is especially worthwhile with legislators whose districts are far from the capitol.
• If a committee or legislator tours you campus: plan their visit to the minute, make sure any local legislators are invited, don't overwhelm them with people, and make the visit fun and worthwhile.
• Legislators often like to give guest lectures and teach courses, especially in areas they're personally interested in; this can be a great way to build relationships and get them more involved with your campus.
• The "biggest mistake" most institutions make regarding bond funding is not having a plan "on the shelf" ready to submit; he recommended that all institutions, even if they have just gotten an item funded by a state bond, develop a plan for what their next highest priority is.
• Most decision making at the legislative level is not decided by the local parties, but instead by the caucuses -- the groups of elected representatives that all share a similar party; caucus politics often differ from those of the caucus's party. Your representative will have to justify your case to their caucus, not their party, so learn about the caucus if you can.
• Don't get involved (as an institution) in campaigns or candidate endorsements, primarily because it's possible the opposing candidate will win.
• Avoid the temptation to mail or e-mail documents and items; they will most likely be thrown away or deleted (especially if they look like a mass communication). If possible, personally deliver items or call to talk about the issue.

Categories:

• teaching
• conference
• Innovations
• 2006
• politics
• lobbying