Qwizdom: a very negative first impression

[This post reviews Qwizdom's Q4 RF in-class response system, comparing it with Interwrite's IR in-class response system.]

Introduction:

This semester I'm trying out a new (to me) brand of in-class response system. Today was the first day I used the system live in my class, and things did not go well. Before I talk about what went wrong, let me give readers some background.

In-class response systems are great for encouraging participation in classes. To use the system each student in the room buys (or is given) a hand-held transmitter that wirelessly sends the student's response to a receiver at the front of the room; a computer collects all the answers and then displays a histogram of the students' responses. I absolutely love using in-class response systems, and have written a number of posts on them (see my archive here, or just skip to my summary post of the negatives and positives of the systems). I use these systems primarily to encourage participation and quickly evaluate whether students are understanding the material. My grading is very simple: each question the students answer (correctly or incorrectly) is worth one point.

For the past two years (four semesters), I've used Interwrite's PRS system. Interwrite's student transmitters use infrared (IR) to send signals to the computer's receiver (the transmitters are glorified remote controls). Using infrared to send signals has two big drawbacks: each student must have a direct line of sight to the receiver (and thus multiple receivers must be installed in large rooms), and there is no possibility of two-way communication (e.g., the student transmitters can't confirm that the receiver has received the signal).

Qwizdom's RF unit:

The new system I'm using is made by Qwizdom, and it transmits signals via radio frequency (RF), allowing for non-line-of-sight two-way communication. RF transmitters hold much promise for the future of in-class response systems, if only because installing the system in a large room is as simple as plugging a small receiver into the USB port of a computer.

Qwizdom's Q4 transmitter (seen here) has lots of useful buttons; it comes with a 10-key numberpad complete with dash and decimal point, allowing instructors to ask both multiple-choice questions and numeric questions (which would be great for math or physics classes). Other transmitters on the market (eInstruction's RF unit and Interwrite's IR unit) either offer only multiple-choice answers (A-F; eInstruction) or have a numberpad but lack a decimal point (eliminating many possible numeric answers; Interwrite). Interwrite is coming out with a RF unit that does have a full numberpad with decimal point, but I have not used it.

While RF may be the wave of the future, Qwizdom's product has some major problems:

• Price: the student transmitters are sold to bookstores for $49 each; after the bookstore marks them up they'll probably sell for well over $50, making them prohibitively expensive (if I hadn't been able to give each student a free transmitter this semester, I wouldn't be using the system).
  
• Student ease-of-use: I spent more than 20 minutes in lecture today trying to show the students how to use the system and ask my first two questions. Students have to enter both a session ID and a student ID to use the system; many students had trouble doing this.
• Software: Interwrite's software was bad enough that I complained about it in this post, but Qwizdom's (Qwizdom Interact v2.1) is far worse. In fact, I'd say it's awful. I spent hours this week attempting to beat it into doing an extremely simple task, and even with tech support's help it still failed.
  

Qwizdom's Software:

By far the largest negative about Qwizdom's system is the software (though the price of student remotes is also far too high). In-class response system software has two basic tasks: to facilitate asking questions during a lecture (or other meeting) and then collate the data gathered and display it in a graphical form in class (e.g., a graph of student responses) and in a textual form after class (e.g., transfer it to a grade book or allow it to be exported to be analyzed by other programs). Qwizdom's software does none of these well.

The first problem with Qwizdom's software came when I attempted to try it out in my office. It became apparent that if I wanted to record the answers each transmitter submitted (and associate them with some ID number) then each user of the transmitter needed to log in with a user ID. Each user had to have an ID created in the software before the user could log in. The software does have the ability to import data from csv files, but only in a very defined format (about a 10 column-wide spreadsheet, one of whose required columns is gender), and thus I had to convert my roster into their format.

The requirement to have each user of the system already in the program's database before they can use the system is extraordinarily annoying. First, it absolutely prevents use of the system in the first week or two of the semester, as students may not even be officially enrolled in the class, and thus instructors wouldn't know to add them to the system. Second, it means that instructors have to tediously enter student data into the system. It would be much better if users could key in their ID numbers and names whenever they joined a session that they weren't already users in.

There is a way to allow an audience to not have to log in with user IDs, but if this method is used, each transmitter is assigned an (apparently) random ID number; this ID number varies between sessions, meaning that there is no way to track each student's use of the system and thus no way to evaluate student performance.

As a side note, Interwrite's system gets around this entire user ID problem by assigning each transmitter a factory-specified unique ID number that is always stored along with the answer the transmitter submits (so even if you never know who was using the transmitter, you can at least track that transmitter's answers between different sessions).

But getting student IDs into the program was only the first headache. After I did that, my next goal was to figure out how to ask a quick question in lecture. To give a little more background, I have embedded my in-class response system questions into my PowerPoint lecture slides; I go through around 25 to 35 slides per lecture, with maybe 2-5 question slides. This adds up to more than 800 slides over the course of the semester and more than a hundred individual questions. In other words, I've put a lot of work into my PowerPoints, and I'm not about to change programs anytime soon. But that's exactly what Qwizdom's software mandates - their program is designed solely to ask questions that users have presented using their in-program presenter (a complicated-looking clone of PowerPoint). To ask questions you have to make a slide for every question, and specify on that slide exactly what the answer is.

The software does have the ability to ask spontaneous questions that haven't been entered in advance (which eliminates the requirement to use their presenter program), but using this option has its own problems. First, the program doesn't store spontaneous question responses in the gradebook, and doesn't make them available anywhere for review. The only place the responses are stored is a csv file in the program's system directory tree, but even in that file the responses have been separated from the student IDs. And, even worse, when the spontaneous question option is used, the program's control window (which takes up the top 1/6th of the screen) is hard-coded to show up in front of all other Windows' windows, including full-screened PowerPoint slideshows. In short, the spontaneous question portion of the program is functionally useless.

The only solution I could come up with to allow me to ask the questions built into my PowerPoint lectures was to create a dummy presentation in Qwizdom's system with blank questions in it. I showed my PowerPoint slideshow in front and ran Qwizdom's software in the background, but even this worked poorly. Qwizdom's software wanted to run full-screen; when I shrunk it down so it only filled half the screen, the font in Qwizdom's screen distorted awfully, and the response graph was created off-screen. So, what I had to do today in lecture was ask the question in PowerPoint, then alt-tab out to Qwizdom's screen, un-maximize Qwizdom's window and resize it so that it only filled half the screen, wait for students to respond, re-maximize Qwizdom's window, click on a menu item to show the student response graph, click on another menu button to close the response graph, and finally alt-tab back into PowerPoint to continue my lecture. Clunky, slow, and stupid.

Even more hilariously, Qwizdom has a built-in timer that counts down when you start a question; when the time reaches 0 a big "Time's up!" gray window pops up for a few seconds. However, students can still answer the question after "Time's up!", and the time is not adjustable at all during the presentation (it's set only when the entire presentation starts); there is no way to pause, extend, or otherwise change the time per slide during a show. I asked Qwizdom's tech support about this and they reported that it was just a dummy timer that I should ignore. Useless.

In contrast, while I still had to run Interwrite's software in the background behind my PowerPoint slideshows, it didn't require me to make a dummy presentation, didn't need to be un- and re-maximized for each question, had an extremely easily adjustable timer (time for each question could be adjusted by 15-second increments both before a question was asked and while the time was counting down), and the response graph auto-popped up when the timer hit zero.

Even after I clunked my way through the lecture, I still ran into one last problem: the software requires that each question have one right answer worth some set value of points and some wrong answer worth fewer points. Since I want every student to get a point for the question even if they didn't get the right answer, this means that I can't even use my grading scheme with this software. The program did allow me to leave the answer to a question blank (not set), but whenever I did that the question became worth 0 points, and so the gradebook showed 0's for every student in my course, regardless of how many questions they answered. The program won't even tell me how many questions each student answered.

Conclusion:

On the surface, Qwizdom's system appears to be extremely polished. The hardware looks very modern and is very functional. However, Qwizdom's software is atrocious. The software might be OK if you were doing some pre-programmed corporate spiel and didn't mind using Qwizdom's built-in presenter, but it utterly fails when presenting with PowerPoint or whenever you want to do anything even slightly out of the ordinary.

In fact, this week's experiences have been so bad that I have no hesitation whatsoever in giving Qwizdom's product my first-ever Radagast Stamp of Disapproval.

Growing ferns

I'm going to start this honestly: I have no idea how to grow ferns from spores. This probably explains why I'm crazy enough to try to figure out how to do it with my class.

Why would I want to bother rearing ferns in class? Well, ferns (like all other non-seed plants like mosses and liverworts) don't reproduce via seeds; instead, they produce haploid spores that fall to the ground and grow into little haploid plants called gametophytes (termed prothalli in ferns). These haploid gametophytes produce gametes (sperm and eggs), and just like in animals, the sperm swim to the egg and fertilize it. Once the egg is fertilized (and thus diploid), it grows into a sporophyte, the leafy part of a fern most people recognize.

As a quick side note, most folks (reading this blog) probably know that animal gametes (sperm and eggs) are produced by meiosis, a process wherein a diploid cell divides and becomes four haploid cells. However, fern gametes are produced by mitosis, not meiosis. The reason fern gametes are produced by mitosis is that they're created by gametophytes, which themselves are haploid (have only one copy of each chromosome), so going through meiosis would be impossible for the cells in the gametophyte. In ferns, meiosis is used by the diploid sporophyte to produce haploid spores (which grow into the gametophyte that eventually creates the sperm and eggs).

Non-seed plant life cycles are pretty cool, but unfortunately teaching about them is generally dull. I show my students a few figures, they look at a few slides of cross-sections of plant reproductive organs, see the sori (which contain sporangia that produce spores) on the underside of fern fronds, observe a little preserved gametophyte, and we all agree that we've learned how non-seed plants reproduce. But that's always seemed somehow insufficient.

So, what I'd like to do is have the students actually rear ferns. It seems as though it's at least possible; these three sites have good summaries of how to rear ferns in layman's terms, and from what I can tell it primarily requires spores, sterile soil, and lots of time (anywhere from two months to a year). Assuming we could go from spore to small sporophyte in two months, I could fit that into a single semester; the students could plant the spores at the beginning of the semester and then, if we're lucky, see mature sporophytes popping up at the end of the course. Maybe the students could even take home their little sporophytes at the end of the semester. Watching the gametophytes grow wouldn't be quite as dramatic as watching the caterpillar Manduca sexta going from a 1-mg egg to a 5-g pupa in three weeks (see my series of posts on that here), but it'd still be cool.

The American Fern Society has a spore exchange that supplies spores to people, and even has its own detailed set of rearing instructions. Unfortunately, however, I haven't been able to find any estimates of the time it takes specific species to go from spore to gametophyte to sporophyte, and thus don't know what species would be best to use. Looks like I've got some research to do.

Colorblindness in heterozygous females?

Nelumbo, of Biology Educators, has a good genetics question:

1. Red/Green colorblindness can be a x-linked trait.
2. If my husband has this type of color-blindness, our female child would have his 'mutant' X chromosome.
3. Let's assume I do not carry the trait and donate an 'normal' X chromosome for the trait.
4. Our daughter would be heterozygous for the trait, or a carrier.
5. One of each of her X chromosomes would be randomly inactivated in each cell

so....

Would about half of her optical cells show the normal protein? Or is the inactivation early in development, so all her optical cells would be the same ( either all maternal or paternal X inactivated)? Or even weirder yet, could she be colorblind in just one eye?

I'm no expert in developmental genetics (PZ, where are you?), but I can at least take a stab here. X-chromosome inactivation is the name of the phenomenon wherein one copy of the two X chromosomes found in a female's cells is inactivated by turning the chromatin in the chromosome into heterochromatin, preventing gene expression. X-chromosome inactivation occurs in both insects (e.g., Drosophila) and mammals.

To answer Nelumbo's question, the matter of when the X chromosome inactivates is important. If the X chromosome is inactivated early in development, then large patches of cells should have the same X chromosome expressed; if the X chromosome is inactived late in development, then each cell might express a different copy of the chromosome than its neighbor. I dug out my old developmental biology textbook (Gilbert 1994), brushed off the dead Drosophila, and found this experimental answer to the question:

One of the earliest analyses of X chromosome inactivation was performed by Mary Lyon (1961), who observed coat color patterns in mice. If a mouse is heterozygous for an autosomal gene controlling hair pigmentation, then the mouse resembles one of the two parents or has a color intermediate between the two. In either case, the mouse is a single color. But if a female mouse is heterozygous for a pigmentation gene on the X chromosome, a different result is seen: patches of one parental color alternate with patches of the other parental color.

So, the X chromosome inactivates early (within 10 days of the start of gestation in mice), and thus large patches of cells have the same X chromosome inactivated. The same type of system is responsible for the pattern of female calico cats.

This means that it's likely that large patches of Nelumbo's heterozygous daughter would have the same X chromosome expressed, and thus it seems at least possible that her daughter could be at least partially colorblind. This conclusion is backed up by this website:

Red-green colour blindness is hereditary and is passed via the X chromosome. Women, who have two X chromosomes, are usually not colour blind. But about 15% of them are carriers (i.e., they inherit an X-chromosome carrying an abnormal photopigment gene array from one parent) and may share in part in the colour blindness that they pass on to their sons, owing to a process of dosage compensation known as X-chromosome inactivation of lyonization.

This wikipedia entry also confirms that X-chromosome inactivation does change the color vision of carrier females; it implies that there is variation in the receptors present in each eye, and thus the female shouldn't be completely colorblind. However, I haven't found a good reference clearly explaining the range and frequency of clinical symptoms observed in females heterozygous for red-green colorblindness.

So, I leave it up to the rest of you great geneticists (and medical folks) to provide more details.

Reference:

Gilbert, Scott F. 1994. Developmental Biology 4th edition. Sinauer Associates, MA.

Wikipedia being edited by congressional staffers

Wikipedians recently noticed that Congressional staffers appeared to be editing Congress members' Wikipedia entries. Normally this wouldn't be a bad thing, except that at least some of the staffers weren't editing according to Wikipedia guidelines (e.g., including only documented facts). The Wikipedia has a request for comment on Congressional staffers' edits (linked to by slashdot), and this newspaper article has more. WikiNews also has an article detailing many of the edits, as well as how wiki investigators discovered who was editing what (via DisinterestedParty and BoingBoing).

Orac moves to a new home

Sheesh, it seems like all the cool bloggers are moving over to ScienceBlogs. Orac, who blogs at Respectful Insolence, has moved from his old blogger blog to a new ScienceBlogs blog; his new url is: http://scienceblogs.com/insolence/. Orac discusses the move here and here.

Reagular readers should have no fear: I'm in no danger of going over to ScienceBlogs anytime soon. This is partially because I'm most certainly not cool, but also because I'm not sure that I like the idea of turning this into a commercial venture with ads all over the place. Oh yes, and then there's that little detail that, even though I'm a scientist, I often get distracted and don't post about science.

Homemade applesauce

A few years back (before we lived in Southern California), I got extremely ill on a trip to the area. We ended up heading to a friend's house, where I was miserable and couldn't keep any food down for about a day. Once I was feeling a little better, my SO and friend headed out to a local grocery store to buy something inoffensive for me to eat; they chose some generic applesauce. They put a little bit in a bowl for me to try; it was the best-tasting food I have ever eaten. It was like someone had hand-selected the most flavorful apples ever grown, mixed them with the most delicious sugar, and then used some sort of magic to top it off.

Of course by the next day the applesauce tasted just like any regular applesauce, but I've always wanted to have that perfect applesauce again, and today I came about as close as I suspect I ever will. We had about three pounds of apples just sitting around getting old, so we decided to make some applesauce with them (based on a recipe in Joy of Cooking). After a few minutes of peeling, and about half an hour of cooking, we had a pot of absolutely delicious applesauce. Since the applesauce was so good, it's this week's end-of-the-week recipe blogging post.

3 pounds apples (cored and, optionally, peeled)
1 to 1 1/2 tablespoons lemon juice
1/2 to 3/4 cup apple juice or cider
1 cinnamon stick (~3" long)
Scant 1/2 cup sugar (Joy reports you can also use 6 tablespoons honey)

1. Slice the apples into 1/2"-thick slices.
2. Put the apples, lemon juice, apple juice, and cinnamon stick in a pot and bring to a simmer, covered, over medium-high heat.
3. Simmer, covered, for 20 minutes (or until the apples are soft), stirring occasionally.
4. Add the sugar and stir to mix; remove the pot from the heat once the sugar is dissolved.
5. Mash the apples to whatever consistency you desire; we stirred it with a spoon until we had a coarse applesauce, but you could also mash it with a potato masher or put it in a blender or food processor for a finer applesauce.
6. Serve warm or cool (we loved it warm).

Notes:

Joy of Cooking recommends using a mix of apple varieties for the best flavor; we used all Golden Delicious and it was, well, delicious. Joy says to vary the lemon juice amount with the tartness of the apples, and the apple juice amount with the juiciness of the apples; it also suggests that you can add extra flavorings if you desire (1/2 teaspoon nutmeg, 1/2 teaspoon ground mace, and 1/2 to 1 teaspoon ground ginger).

See the notes of this post for more information on buying apple juice.

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

Happy Birthday, Chuck

Pharyngula reminded me that today is Charles Darwin's 197th birthday (aka Darwin Day). PZ has a nice picture posted, as well as a few other posts (young Darwin and Eldredge on Darwin); The Questionable Authority has a list of other posts.

Unfortunately, my SO and I have no celebration planned. I spent the day upgrading my TWiki install to version 4.0 (a much easier-to-use version, from what I can tell; read about how I use it here), and will be spending the evening at work.

Weekend humor

Biology Educators had a brilliant idea to make a quick million, discovered that you can supposedly buy a hernia on eBay, and also offered a few good answers to the eternal question of what's a weed?

Pharyngula has linked to excerpts from the new Christian science textbook.

BoingBoing has linked to an anagram map of tube stations in London.

Botanical Girl's in trouble

I've been fuming ever since I read Botanical Girl's post Bridges Burned. Unfortunately, only now could I sit down to blog on this. Here goes:

A few days ago I linked to a post by Botanical Girl (a pseudonymous blogger) titled "What not to do on a faculty interview" (link no longer works; Botanical Girl has deleted the post), wherein Botanical Girl reported on shortcomings in a recent job candidate's talk. The post briefly summarized the situation, and then went on to outline some of the mistakes Botanical Girl felt the speaker had made.

Unfortunately, as one can read about in Botanical Girl's latest post, this has turned into a huge mess. As a result of her post, Botanical Girl was outed to her department and the job candidate, and is "now in the unenviable position of being the cause of an embarrassing situation for [her] entire department."

It's clear from her post that Botanical Girl is in a great deal of trouble; she says that her graduate school advisor "may wind up taking heat for [her] actions", reports that her original post has been taken to be "insulting", and as a result of all of this she's not sure that she'll continue blogging.

I believe very strongly that Botanical Girl has done nothing wrong in this situation; the post should never have been deleted, and she has nothing to be embarrassed or ashamed about. All Botanical Girl did was write a critique of a public talk; she did not include any personal attacks or smears of any kind, and simply related what she felt could have been done to improve the talk. That's it.

Making the situation even more interesting, Botanical Girl was completely anonymous until this event; she never used her name on her blog, and the only identifying information easily available on her blog was that she lived in California. Botanical Girl also never named the candidate; it's hard to smear someone you don't name when you write anonymously. Yet apparently some in her department believe that she has soiled the department's reputation. This view seems to be strong enough that Botanical Girl feels she must add the disclaimer "the views and opinions expressed here are solely my own, and do not reflect the views of my department and my school" to her blog. The idea that such a disclaimer might be needed is ridiculous; how could an anonymous blogger's opinion be considered to represent the department she's working in when she doesn't even say what school she's at?

But the issue of Botanical Girl being anonymous is actually beside the point; even if Botanical Girl posted under her true name and listed the name of the speaker, the post would still have been perfectly reasonable. Here's an example of the comments Botanical Girl made:

[Thing not to do #3].Make negative comments about your assistants
This is the one that really bugged me. Candidate put up a slide with some preliminary data: GUS localization on other genes in the same family. The images were quite intriguing and seemed to fit with the presentation. Until candidate remarked that "these were done by an undergrad and well...(big pause)....I'd really like to re-do them." Honestly I can't remember if they said they thought they were bad or just that theyd like to repeat, but the intention was there. Clearly this person does not trust the work done, and yet they put the images in a presentation for an interview. Either you stand by your work or you don't. Don't waffle around. If you don't trust the results you should have confirmed them before you left, or at the very least kept your mouth shut. I can't tell who stained the tissue from the picture. If you're knocking your colleagues now, why won't you do it to your post-docs and grad students when you get a professorship?

There's nothing personal in that statement; all that's there is a statement of what Botanical Girl believed to have occurred in the talk, and her response to that occurrence in terms of how she feels talks should be given. It may not be written in the exact style I'd use, but how is this embarrassing to the department? Is it somehow wrong to give someone negative feedback? It shouldn't be, but it sure feels like that's the reason Botanical Girl's in trouble.

When I re-read Botanical Girl's original post yesterday evening I noticed that the original speaker had posted a reply to Botanical Girl's comments. The reply was professional and attempted to clarify the speaker's intentions in the talk. While Botanical Girl may not have been intending to get a reply from the original speaker, this reply could have been the start of a very interesting discussion. Instead, now the discussion will not occur because it has been killed by departmental criticism of Botanical Girl.

Unfortunately, Botanical Girl has not passed her oral exams, so she's in a very tenuous position politically. It's unclear what the best course of action for her in this situation would be, but I think it would be a shame if she were to be forced to stop blogging simply for posting honest feedback about a public talk.

Snails are faster than ADSL

Researchers at KinnerNet have developed a snail-based data transfer protocol (SNAP), and have proven beyond a hair of doubt that snails do indeed transfer data faster than both carrier pigeons and ADSL. This summary article is hilarious, as is the full paper (PDF) that details the new protocol (both include great pictures).

(Via BoingBoing)

Today's outline

Time spent teaching: 3 1/2 hours
Time spent in meetings and otherwise being department chair: 6 1/2 hours

Oh well ...

A few links

I once again have very little time on Tuesday and Thursday nights to blog (thanks to late-night Tuesday and Thursday classes followed by annoyingly early Wednesday and Friday classes), so here are a few links to keep you occupied:

Orac has two good articles on alternative medicine: Ineffective alternative medicine is not always harmless and Coretta Scott King: A victim of alternative medicine?

PZ Myers linked to a Carl Zimmer article about the wonder of leeches. Having seen leeches in a lab that reared them, I must agree with PZ that they do have a sleek beauty to them.

BotanicalGirl talks about what not to do on a faculty interview, while profgrrrrl discusses what not to do in your tenure packet.

And, regarding the newly proposed federal budget, PZ Myers reports that Bush is proposing the ridiculous with education, EduWonk has even more details on proposed education spending, Respectful Insolence reports that the proposed NIH budget is frozen, and the House Democrats have a page contrasting Bush's 2006 State of the Union Address claims with the reality of Bush's actions in 2005.

[Update Feb 10, 2006: BotanicalGirl's post has been deleted and she's now in trouble with her department; see this post for more details.]

Plitvice Lakes

Over the weekend I saw a Nature program highlighting Croatia's Plitvice Lakes National Park; it's a UNESCO World Heritage site, and appears to be very biologically diverse and picturesque (do a Google image search to see for yourself). The Nature program (as usual) focused overwhelmingly on the vertebrates; I'd love to get a chance to see the invertebrates (not to mention organisms from the other five kingdoms) that were there.

Yogurt braised chicken (Dahi murghi)

This past week was filled with the usual start-of-the-semester stress, but it had two additional components that made it even more stressful: a contractor was building a new block wall in our yard, and my mom came into town for a short visit. My mom arrived Wednesday night and I wanted to make her a tasty meal, but I didn't have much time, and many of our standard quick recipes didn't work due to my mom's dietary restrictions.

We're still on our Indian food kick, so I eventually settled on Sahni's (1980) yogurt braised chicken. The dish is made by simmering chicken in an onion- and spice-rich yogurt mixture, and it was extremely flavorful, yet very easy (for Indian food). It took me, working alone from scratch, less than an hour to do all the prep work and initial cooking, and then the dish just simmered for 45 minutes while I did a little bit of last-minute cleaning.

When my mom arrived, she enjoyed being greeted by the delicious smell of the dish simmering, and after dinner reported that she loved the meal. So, this is this week's end-of-the-week recipe blogging post.

1/2 cup vegetable oil
3 cups finely chopped onions
1 1/2 tablespoons garlic, minced or pressed with a garlic press
1 tablespoon ground coriander
1/2 teaspoon cayenne pepper
1 1/2 teaspoons garam masala
1 teaspoon roasted Indian poppy seeds (they should be small and white, not the blue ones typically found in American stores; likely optional)
1 cup plain, whole milk yogurt
1/4 cup sour cream
1/3 cup water
1 tablespoon Kosher salt
2 pounds boneless, skinless chicken thighs (or ~3 pounds bone-in chicken pieces)
Cooked rice, or Indian bread, to serve over

0. Plan on having some rice or Indian bread cooked by the time the dish is ready to serve.
1. Heat 1/4 cup of the oil over medium-high heat in a large nonstick pot.
2. When the oil is hot, add the onions to the pot and cook, stirring frequently, until they begin to brown (~10 minutes).
3. Add the garlic to the pot and cook, stirring frequently, for 2 minutes.
4. Add the coriander, cayenne pepper, garam masala, and poppy seeds, and cook, stirring frequently, for another minute.
5. Add the yogurt, sour cream, and water, and simmer, covered, for 5 minutes.
6. Remove the yogurt mixture from the pot and blend until smooth; we used our immersion blender in a small bowl, but a blender should also work well. There's no requirement to do this quickly, as it won't be needed for another 5 or 10 minutes.
7. Wipe the pot you were using so that it's somewhat clean (or use a new pot), add the remaining 1/4 cup of oil, and heat over high heat.
8. When the oil is hot, add the chicken and cook, turning occasionally, until it is browned on most of the sides (~5-10 minutes).
9. Add the blended yogurt mixture to the pot, mix in the salt, and simmer, covered and stirring occasionally, for 45 minutes. Sahni states that "the [sauce] should have thickened to a velvety smooth white sauce, and a glaze will be coating the chicken pieces"; you can simmer the dish for additional time, or add water or milk, to adjust the texture to your preference.
10. According to Sahni, the dish tastes best after it has rested for a while; we let it sit, covered, for about an hour, but it would probably be OK to eat right after simmering.
11. Reheat the dish and serve over rice or with Indian bread.

Notes:

We have no idea how much the Indian poppy seeds add to the dish; if you don't have them, try making the dish anyway. If you can't find Indian poppy seeds at your local store, Penzeys Spices has them (here). To roast raw poppy seeds heat them in a pan over medium heat until they begin to turn brown and become fragrant.

The amount of oil included in the recipe is the full amount Sahni specifies; I suspect you could cut out a tablespoon or three of oil and the dish would be just as good.

Reference:

Sahni, Julie. 1980. Classic Indian Cooking. William Morrow & Co, NY. pp. 211-213.

Some Saturday humor

A parody of what different skeptics (and not-so-skeptics) would write about why the chicken crossed the road; the parody of Respectful Insolence is great (and located near the bottom of the post; via Pharyngula).

And, speaking of Pharyngula, go read a description of an event he did not attend.

A parody of Bush's 2006 State of the Union address (via DailyKos, posted before Bush's speech).

Bush's NSA spying defense doesn't hold up

The New York Times has written an editorial thoroughly debunking the Bush administration's justifications of the NSA's warantless wiretapping.

A bit over a week ago, President Bush and his men promised to provide the legal, constitutional and moral justifications for the sort of warrantless spying on Americans that has been illegal for nearly 30 years. Instead, we got the familiar mix of political spin, clumsy historical misinformation, contemptuous dismissals of civil liberties concerns, cynical attempts to paint dissents as anti-American and pro-terrorist, and a couple of big, dangerous lies.

The full editorial is a good summary of the situation, and it ends with a strong call for Congress to take action:

The Senate Judiciary Committee is about to start hearings on the domestic spying. Congress has failed, tragically, on several occasions in the last five years to rein in Mr. Bush and restore the checks and balances that are the genius of American constitutional democracy. It is critical that it not betray the public once again on this score.

(Via Representative Conyers's blog and my SO's mom, who made me aware of the editorial within about five minutes of each other.)

Police arrest Cindy Sheehan for wearing a T-shirt, then say it was a mistake

The Capitol Police arrested Cindy Sheehan last night before Bush's State of the Union Address for wearing a T-shirt listing the number of soldiers killed in Iraq. This MSNBC story, when read yesterday, included the following summary:

Sheehan, who was invited to attend the speech by Rep. Lynn Woolsey, D-Calif., was charged with demonstrating in the Capitol building, said Capitol Police Sgt. Kimberly Schneider. The charge was later changed to unlawful conduct, Schneider said. Both charges are misdemeanors.

The T-shirt bore the words "2,245 Dead — How Many More??" in reference to the number of U.S. troops killed in Iraq, protesters told NBC News.

Police handcuffed Sheehan and removed her from the gallery before Bush arrived. Sheehan was to be released on her own recognizance, Schneider said."

However, the MSNBC story has now been edited to reflect that the Capitol police made a mistake and that Cindy should never have been removed from the building. Reuters has left up an unedited version of the story, and the MSNBC story now reads:

Capitol Police dropped a charge of unlawful conduct against antiwar activist Cindy Sheehan on Wednesday and apologized for ejecting her and a congressman’s wife from President Bush’s State of the Union address for wearing T-shirts with war messages.

"The officers made a good faith, but mistaken effort to enforce an old unwritten interpretation of the prohibitions about demonstrating in the Capitol,” Capitol Police Chief Terrance Gainer said in a statement late Wednesday.

"The policy and procedures were too vague," he added. "The failure to adequately prepare the officers is mine."

...

"Neither guest should have been confronted about the expressive T-shirts," Gainer’s statement said.

Quick reads

My mom just arrived today for a short visit. That, combined with the wall construction that is still ongoing (and waking us up every morning at 7am), is making the first week of the semester busier than usual. However, to keep my dedicated readers occupied (and continue on my recent political posting streak) here are a couple of quick links:

John Conyers reports:

In what has been described as "highly irregular," email correspondence from vice-president Cheney's office during the period of the Plame leak appears to have been deleted. Correspondence generated in the official duties of the President and Vice-President becomes the property of the National Archives and does not belong to the chief executives.

While Special Prosecutor, Patrick Fitzgerald, has not accused the Vice-President's office of wrongdoing, Steve Aftergood, director of the Federation of American Scientists government secrecy project has called the destruction of this specific subset of communications "highly irregular and invites suspicion."

Pharyngula takes a close look at the scientific implications of just one small bit of Bush's State of the Union Address and finds that Bush is proposing policies that would drastically hinder progress in medical research.

The joyous first week begins

Things are back to usual here at Rhosgobel, as classes have started again; I just met my lecture students for the first time today. I was asked many spontaneous questions during the lecture; all of them were relevant to the topic at hand, and some were quite advanced. I couldn't have asked for a better first lecture.

It's been an interesting past few months; back in October our spring schedule was cut by a large fraction for budgetary reasons, but in the past few weeks the administration has realized that enrollment is now way down (gee, never would have expected that ...), and thus the administration has been frantically asking us to add lab sections. Adding labs at the last minute is an administrative disaster, as we have to find adjuncts to teach the labs, arrange for lab techs to support the labs, order supplies to teach the labs, and find timeslots to fit the labs in (oh yes, and notify the students that the new lab exists). My department has pulled through amazingly and added four new labs, two of them just in the past week. I'm so proud!

Other administrative headaches are also piling up and distracting me from teaching. Probably the largest is that the administration already wants both next summer's and next fall's schedules drafted out within the next few weeks. The fun never ends!

Why is this only being reported now?

CNN's big headline this morning read "FEMA's big kiss-off?"; it was positioned above a picture of a stranded Katrina victim captioned "Some loss of life 'might not have occurred,' senator says."

While I appreciate that CNN is covering the story about turned-away Katrina aid, it makes me wonder why that headline and provocative quote weren't present in the weeks after the hurricane (when, for instance, I was able to easily collect more than 20 unique reports of denied Katrina aid; see this post for the full list).

The CNN article appears to have been spurred by the investigations of a congressional committee into the response to hurricane Katrina (the committee is summarized here, and its hearings are detailed here). The CNN article does have some new information in it; for instance, the committee has uncovered evidence that FEMA even rejected offers of aid that came from within the US government.

The Interior Department offered FEMA 500 rooms, 119 pieces of heavy equipment, 300 dump trucks and other vehicles, 300 boats, 11 aircraft and 400 law enforcement officers, according to a questionnaire answered by a department official.

Interior law enforcement officers included special agents and refuge officers from the department's Fish and Wildlife Service.

"Although we attempted to provide these assets, we were unable to efficiently integrate and deploy these resources," an Interior Department official wrote the Senate committee investigating the government's response to Katrina.

...

[Within three days of the hurricane landing,] the Interior Department had offered FEMA hundreds of law enforcement officers trained in search-and-rescue, emergency medical services and evacuation, according to the documents.

"The Department of the Interior was not called upon to assist until late September," the Interior official writes.

The hurricane made landfall on August 29.

The chair of the investigatory panel (Senator Susan Collins) seems to be (understandably) outraged:

"Now, you might be able to understand if it came from outside government," she said. "But this is another federal agency, an agency that was offering trained personnel and exactly the assets that the federal government needed to assist in the search-and-rescue operations."

Circuses of the spineless

PZ Myers has posted two versions of the Circus of the Spineless: the first is the (more traditional) biological version, and the second is a special Senate version.

A bit of advance notice might have been useful ...

While reading Orac this morning I discovered that today was "International Internet-free Day". Well, so much for that idea.

An imprecise watch

BoingBoing has a summary of a very snazzy idea: a watch that displays time in imprecise units like "Around 6 Fifteen" and "Just Before 7". Apparently you can get a plugin to do this on your Mac menubar; I wonder if there's a Gnome/X-windows plugin for it.

Kerry's speech on Alito

Last night on CSPAN (yes, I've taken to watching CSPAN), I watched most of John Kerry's speech on why he's filibustering Alito; the speech was well-delivered and information-rich, and the full text is available online. Here's an excerpt:

"In 1984, for example, Judge Alito wrote a Justice Department memorandum concluding that the use of deadly force against a fleeing unarmed suspect did not violate the fourth amendment. The victim was a 15-year-old African American. He was 5 foot 4. He weighed 100 to 110 pounds. This unarmed eighth grader was attempting to jump a fence with a stolen purse containing $10 when he was shot in the back of the head in order to prevent escape. The Sixth Circuit Court of Appeals found the shooting unconstitutional because deadly force can only be used when there is 'probable cause that the suspect poses a threat to the safety of the officers or a danger to the community if left at large.' That is what we teach law enforcement officials.

"But Judge Alito disagreed. Judge Alito said: No, he believed the shooting was reasonable because 'the State is justified in using whatever force is necessary to enforce its laws'--even deadly force. That is his conclusion. That is the standard that is going to go to the Supreme Court if ratified. It is OK to shoot a 15-year-old, 110 pounds, a 5-foot-4-inch kid who is trying to get over a fence with a purse, shoot him in the back of the head.

...

"Perhaps Professor Liu of the Berkeley Law School put it best when he wrote this. He said:

'Judge Alito's record envisions an America where police may shoot and kill an unarmed boy to stop him from running away with a stolen purse; where federal agents may point guns at ordinary citizens during a raid, even after no sign of resistance; where the FBI may install a camera where you sleep on the promise that they won't turn it on unless an informant is in the room; where a black man may be sentenced to death by an all-white jury for killing a white man, absent a multiple regression analysis showing discrimination; and where police may search what a warrant permits, and then some. This is not the America we know. Nor is it the America we aspire to be.'"

Google China

Much media hay was made of Google's recent decision to launch google.cn, a Chinese version of their search engine that censors (or, in Google's terminology, "filters") search results. Today Google posted a detailed article outlining their reasoning for bowing to Chinese censorship. Of note is a part of the story that isn't being reported heavily:

... Chinese regulations will require us to remove some sensitive information from our search results. When we do so, we'll disclose this to users, just as we already do in those rare instances where we alter results in order to comply with local laws in France, Germany and the U.S.

As an example, the search results for "tiananmen" are drastically different in the Chinese and English versions, but there appears to be text at the bottom of the Chinese page that indicates the search has been censored (babelfish translates the text as "According to the local law laws and regulations and the policy, the part searches the result not to demonstrate. You are not must look: Tiananmen").

It'll be interesting to hear what Semantic Compositions has to say on the topic, as he's previously talked about Google's censorship of US search results.

You know blogs are big when ...

... the source the New York Times uses to report that a senator (John Kerry) has called for a filibuster is that senator's personal post on a blog (Daily Kos; Kerry's post can be found here).

The issue, of course, is the confirmation hearing of proposed Supreme Court justice Samuel Alito; see this New York Times editorial for why some might want to fillibuster Alito.

Surveilling Americans

The ACLU of Georgia has filed a lawsuit alleging that the government has been secretly surveilling peaceful protests. The lawsuit is based on the questionable arrest of two activists after they wrote down the license plate number of an undercover Homeland Security agent taking pictures of the protest. WXIA news has a story on the suit:

Two documents relating to anti-war and anti-government protests, and a vegan rally, prove the agencies have been "spying" on Georgia residents unconstitutionally, the ACLU said. (Related: ACLU Complaint -- PDF file)

For example, more than two dozen government surveillance photographs show 22-year-old Caitlin Childs of Atlanta, a strict vegetarian, and other vegans picketing against meat eating, in December 2003. They staged their protest outside a HoneyBaked Ham store on Buford Highway in DeKalb County.

An undercover DeKalb County Homeland Security detective was assigned to conduct surveillance of the protest and the protestors, and take the photographs. The detective arrested Childs and another protester after he saw Childs approach him and write down, on a piece of paper, the license plate number of his unmarked government car.

...

The government file lists anti-war protesters in Atlanta as threats, the ACLU said. The ACLU of Georgia accuses the Bush administration of labeling those who disagree with its policy as disloyal Americans.

The ACLU has the full text (PDF) of its complaint online; it contains a detailed narrative of the events surrounding Childs' arrest (starting on page 6).

Ah, satire

Fafblog has recently posted two good satirical pieces; the first is an explanation of recent Democratic party behavior, and the second is a Q&A session about Bush's NSA wiretapping program. I'll steal BoingBoing's quote from the second article as a small sample of what awaits on the other side of the links:

Q. ... But is it legal for the president to ignore the law?
A. Maybe not according to plain ol stupid ol regular law, but we're at war! You don't go to war with regular laws, which are made outta red tape and bureaucracy and Neville Chamberlain. You go to war with great big strapping War Laws made outta tanks and cold hard steel and the American Fightin Man and WAR, KABOOOOOOM!
Q. How does a War Bill become a War Law?
A. It all begins with the president, who submits a bill to the president. If a majority of both the president and the president approve the bill, then it passes on to the president, who may veto it or sign it into law. And even then the president can override himself with a two-thirds vote.

What is this, wake up Radagast and SO early month?

Two weeks ago it was collapsing shelves. Today it's someone using a sledgehammer to knock down our fence. Before 8am. Very loudly.

You'd think we'd be expecting something like that, what with our fence falling down last year and us hiring a contractor to replace it. And you'd be right, except that we were expecting our contractor to show up tomorrow. Not today.

After groggily wandering out into the backyard (and deciding that "What the *$#@ are you doing on my property?" was probably not the best way to start a conversation), I found out that our contractor neighbor had just decided to get things started early. Oh yay. So much for sleeping in.

Something fun

OK, after the last three posts we need something fun here, and thanks to BoingBoing I've got just the thing: Business 2.0's list of the 101 dumbest moments in business of 2005. They also have a (much shorter) list of the smartest business decisions (which can be found via the previous link).

Iraq reconstruction

The LA Times and New York Times both have articles showing that the reconstruction of Iraq is not proceeding as planned. The LA Times reports that oil production in Iraq (which was intended by the US to help fund reconstruction) has decreased:

Iraqi oil production fell by 8 percent last year, with a sharp decline near year's end that left average daily production at half the 3 million barrels envisioned by U.S. officials at the outset of the war in 2003.

Prospects for improvement this year are slim, according to many experts, calling into question Iraq's ability to support itself and fund reconstruction efforts as U.S. assistance is scaled back. Reasons for the shortfall include the poor state of the nation's oil fields, a creaky infrastructure, poor management and ongoing insurgent attacks, particularly to pipelines in the north-central region meant to export oil through Turkey.

...

Oil revenues contribute 94 percent of the fledgling government's budget and a drop in oil global prices from current high levels could wreak havoc if output remains depressed.

The New York Times reports on an audit by the military's Special Inspector General for Iraq Reconstruction (SIGIR) into use of Iraq reconstruction funds:

A new audit of American financial practices in Iraq has uncovered irregularities including millions of reconstruction dollars stuffed casually into footlockers and filing cabinets, an American soldier in the Philippines who gambled away cash belonging to Iraq, and three Iraqis who plunged to their deaths in a rebuilt hospital elevator that had been improperly certified as safe.

...

Agents from the inspector general's office found that the living and working quarters of American occupation officials were awash in shrink-wrapped stacks of $100 bills, colloquially known as bricks.

One official kept $2 million in a bathroom safe, another more than half a million dollars in an unlocked footlocker. One contractor received more than $100,000 to completely refurbish an Olympic pool but only polished the pumps; even so, local American officials certified the work as completed. More than 2,000 contracts ranging in value from a few thousand dollars to more than half a million, some $88 million in all, were examined by agents from the inspector general's office. The report says that in some cases the agents found clear indications of potential fraud and that investigations into those cases are continuing.

...

[T]he portrait it [the audit] paints of abandoned rebuilding projects, nonexistent paperwork and cash routinely taken from the main vault in Hilla without even a log to keep track of the transactions is likely to raise major new questions about how the provisional authority did its business and accounted for huge expenditures of Iraqi and American money.

...

Sometimes the consequences of such loose controls were deadly. A contract for $662,800 in civil, electrical, and mechanical work to rehabilitate the Hilla General Hospital was paid in full by an American official in June 2004 even though the work was not finished, the report says. But instead of replacing a central elevator bank, as called for in the scope of work, the contractor tinkered with an unsuccessful rehabilitation.

For the full-text of the SIGIR audit mentioned in this article, as well as many other SIGIR audits, see this page.

Katrina: investigations hindered and water wasted

Now that I'm back from vacation, it's time to catch up on my political reading. First on my list was catching up on hurricane Katrina news. The New York Times reports that the Bush administration is hindering a Congressional investigation into the response to the hurricane:

The Bush administration, citing the confidentiality of executive branch communications, said Tuesday that it did not plan to turn over certain documents about Hurricane Katrina or make senior White House officials available for sworn testimony before two Congressional committees investigating the storm response.

...

"There has been a near total lack of cooperation that has made it impossible, in my opinion, for us to do the thorough investigation that we have a responsibility to do," Senator Joseph I. Lieberman, Democrat of Connecticut, said at Tuesday's hearing of the Senate committee investigating the response. His spokeswoman said he would ask for a subpoena for documents and testimony if the White House did not comply.

...

[E]ven Senator Susan Collins, Republican of Maine, objected when administration officials who were not part of the president's staff said they could not testify about communications with the White House.

"I completely disagree with that practice," Ms. Collins, chairwoman of the Senate Homeland Security and Governmental Affairs Committee, said in an interview Tuesday.

According to Mr. Lieberman, Michael D. Brown, the former director of the Federal Emergency Management Agency, cited such a restriction on Monday, as agency lawyers had advised him not to say whether he had spoken to President Bush or Vice President Dick Cheney or to comment on the substance of any conversations with any other high-level White House officials.

And, to keep adding to the list of unused aid, the USA Today reported a few weeks ago:

One million cans of drinking water donated for hurricane relief have been emptied and recycled because the water was never used at Texas and Louisiana hurricane shelters, the Federal Emergency Management Agency said.

FEMA hauled the 400,000 liters of water, or 18 truckloads, to a scrap metal business in the Dallas area last month. The water was dumped into a sewer and the cans sent for recycling.

The joys of being department chair

Normally the week before the semester starts is a relatively peaceful one: no students are on campus, and I typically work at home at my own pace. However, on returning from my trip I had two phone messages at home and dozens of e-mails, most of them relating to my role as department chair. The administration has decided it wants to add some classes at the last minute; the department has already found the adjuncts required to do it, but I've got to make sure all of our (already overworked) techs get paid for the extra work they'll be required to do. Also on my schedule for this week is preparing to fight to get a replacement position for a faculty member who's leaving, and trying to figure out how to pay for an unexpected multi-thousand dollar repair bill.

Oh yes, and sometime I should get ready for my courses ...

I'm back!

While my SO and I enjoyed our trip, our house is now filled with many contented sighs as we're both happy to be back home. The trip had lots of fun little tidbits, including:

• Staying with church friends of my mom in upstate New York; we were initially very hesitant to stay with complete strangers, but they ended up being among the nicest people we know. Both were in their 80s (yet are more active than we are), and were great fun to chat with over the breakfasts they kindly made for us each morning.
  
• Once again meeting my great aunt via a trip that entailed both of us traveling many more hours than it would take us to drive to each others' houses.
  
• Having yet more delicious food, including chicken paprikash (a favorite of ours that I've never gotten around to posting), an improvised chocolate version of baked French toast, and a tasty gathering at Buca di Beppo.
  
• Remembering why I love Firefox so much by being forced to use Internet Explorer for days on end.
• Providing a very good excuse for me to avoid reading work e-mail for a full seven days.
  
• And finally, an event that should make PZ proud: we experienced an upstate New York snow storm (~5.5" in one day), and were wandering around in 25F weather many nights on our way back to our lodging. Hats, scarves, gloves, and jackets were worn regularly!

I'll return to regular posting tomorrow; right now it's time to collapse.

It's a bug!

Really! It is! This bundle of cuteness is a hemipteran - a true bug (see this post for more on what a hemipteran is, and why this is one of the only organisms you can actually call a bug).

This is the nymph of a southern green stink bug (Nezara viridula), which I found on my tomato plants this past summer. I took the pictures way back in August, but never got around to posting them, so now that it's winter and I'm on vacation it seems like a perfect time to pull them out.


When I saw this crawling around on my tomato plants I immediately recognized it as a hemipteran, but I had no idea what species it was. After much searching I got the species ID from bugguide.net, where they have pages on hemipterans, stink bugs, and southern green stink bugs. I shouldn't have wasted my time hunting for the ID though, as Urtica posted the species ID as a comment on my Flickr page only minutes after I uploaded it. Thanks, Urtica!


As with all hemipterans, this insect has piercing mouthparts (which you can see in the picture above; the mouthpart is the brown tube reaching back from the insect's head on the underside of its body) that are used for feeding on fluids . In fact, while I was taking pictures I got to see the hemipteran use the tube to feed on a tomato leaf. These bugs feed primarily on tomatoes, and when they feed on the developing fruit of the tomato they can cause it to become disfigured:

When the young green fruit is injured, the cells at the site of feeding are killed by the toxic saliva injected by the bugs into the plant. This area of the fruit stops expanding, while the cells around the dead cells continue to expand by increasing their water content. The result is deformed fruit that appears to have dimples. This type of damage has been called "cat facing." When ripened or nearly ripened fruit is injured, the injection of toxic saliva merely kills a cluster of cells that later forms an off-color hard mass in the fruit, reducing fruit quality and producing a bad flavor to the fruit.

For more information on these bugs, see the Texas Cooperative Extension (where the quote above comes from), the University of California IPM online, and the University of Arkansas Cooperative Extension (which includes pictures of nymphs).


Oh, and if you thought that I was being taxonomically inappropriate with my magazine cover headline, I had these pictures in mind when I created it.

Ants with antibiotics and herbicides

One of the fun biology facts I love to introduce in my biology classes is that humans weren't the first species to develop farming; ants began farming millions of years before our ancestors were even walking bipedally. For example, leafcutter ants (genera Atta and Acromyrmex) bring back pieces of leaves to their nest, which they then use as a medium for growing fungus; the fungus digests the cellulose in the leaves (which the ants can't do alone), and then the ants eat the fungus. The ants even bring fungal spores with them when they start a new nest.

I've known for a while that leafcutter ants weed their fungus farms, but Scientific American's online news has a few neat stories showing that tropical ants use both antibiotics and herbicides to modify their environment.

Some ants rear a type of bacteria that kills other bacteria:

Entomologist Cameron Currie of the University of Wisconsin and his colleagues discovered the antibiotic bacteria in crescent-shaped pits on the exoskeletons of two species of Panamanian ants, Cyphomyrex longiscapus and C. muelleri, after scanning them with an electron microscope. The bacteria--of the Pseudonocarida genus--bloom on the individual face plates and other exterior parts of the ant, allowing it to rub the antiparasitic agent on its fungi crop. The ant also nurtures the microbe by secreting nutrients from special exocrine glands connected to the shallow pits.

And some ants use formic acid as an herbicide:

Sections of the rainforest made-up almost entirely of the tree species Duroia hirsuta, are called "Devil's gardens." Local legend holds that they were produced by an evil forest spirit, report Megan E. Frederickson of Stanford University and her colleagues. But the results of a four-year field study reveal that ants that make their nests in D. hirsuta are the driving force between the homogeneous plots of vegetation. The team introduced saplings of another common Amazonia tree to "Devil's gardens," using a barrier to protect some of them from the ants. Those that were unprotected, however, were quickly attacked by worker ants, which injected poisonous formic acid into the leaves. Trees began to show signs of withering within 24 hours and most of the leaves were lost after five days.

Why Bush's NSA spying program is illegal

Fourteen legal scholars have written a letter to congress detailing why Bush's NSA wiretapping of US citizens without a warrant (which I've written about before) violates existing statute and is almost certainly illegal. The letter is titled "On NSA Spying: A Letter to Congress" and can be found here.

In the letter the scholars provide a lot of background on FISA and relevant Supreme Court decisions, as well as a point-by-point rebuttal of the recent Department of Justice memo (PDF) that attempted to justify the NSA spying program. The letter is well worth reading; here's the conclusion:

In conclusion, the DOJ letter fails to offer a plausible legal defense of the NSA domestic spying program. If the administration felt that FISA was insufficient, the proper course was to seek legislative amendment, as it did with other aspects of FISA in the Patriot Act, and as Congress expressly contemplated when it enacted the wartime wiretap provision in FISA. One of the crucial features of a constitutional democracy is that it is always open to the President—or anyone else—to seek to change the law. But it is also beyond dispute that, in such a democracy, the President cannot simply violate criminal laws behind closed doors because he deems them obsolete or impracticable.

A view of the trip

Last night, while watching "Wal*Mart - The High Cost of Low Price" (a good look at Wal*Mart's bad business practices, though I would have preferred the movie had stuck to presenting the facts of why Wal*Mart isn't a good company and left out some of the attempts at heart-rending stories), my SO's parents' cat decided that she wanted some of my milk:


How undignified.

I'm not going to argue with those teeth ...
Another interesting occurrence was that, on the way home from Sweet Lucy's Smokehouse (an excellent barbeque restaurant in Philadelphia) it got very cold and some white stuff began falling from the sky. The locals informed me that it was called "snow", and made up of frozen water (the craziest things happen when you leave California). After a short while it began sticking to the ground, and when I woke up this morning it was all over the place.


Snow!
The trip has been superb so far from a gastronomic perspective. On the way home from the airport (less than an hour after arriving in Philadelphia) my SO's parents stopped by their favorite local cheesesteak place and picked us up some cheesesteaks (with gooey melted American cheese and fried onions, of course) and a garlic pizza. Then it was fresh bagels the next morning, followed shortly by Memphis baby back ribs at Sweet Lucy's Smokehouse in the evening.

Baked French toast

This has been our only French toast recipe since we first made it a few years ago. Thick slices of bread are soaked overnight in a pan with brown sugar and butter on the bottom and half-and-half and eggs on top, then baked the next morning.


Pouring the half-and-half mixture onto the bread
This recipe is easier than any other French toast recipe we've seen; it does take a bit of planning ahead, but once you've sliced the bread and left it to soak overnight all you have to do is groggily pop it in the oven when you wake up, and 40 minutes later you've got hot, crispy, gooey French toast. We made this for our New Years celebration, but since I was too busy last weekend getting my lab manual ready to write a food post, this is this week's end-of-the-week recipe blogging post.


Hot out of the oven
8 tablespoons (1 stick) butter
1 cup brown sugar
2 tablespoons corn syrup (or honey)
5 eggs
1 1/2 cups half-and-half (or 1 cup milk and 1/2 cup heavy cream)
1 teaspoon vanilla extract
1/4 teaspoon salt
1 pound bread (something like French bread, challah, or ciabatta; don't use bread that has already been sliced for sandwiches)

1. Slice the bread into ~1-inch thick slices (or whatever thickness will allow you to fill a 9x13" baking pan in a single layer).
2. Heat the butter, brown sugar, and corn syrup (or honey) in a small pot over medium heat, stirring regularly, until they are combined.
3. Pour the brown sugar mixture into a 9x13" baking dish.
4. Place the bread into the baking dish, pressing it lightly into the brown sugar mixture.
4. Mix the eggs, half-and-half (or milk and cream), vanilla, and salt in a bowl, and then pour over the bread.
5. Cover and let sit overnight (8 or more hours) in the fridge.
6. Bake in a preheated 350F oven for 40 minutes, or until browned.
7. Serve immediately; we invert the slices so the brown sugar mixture is on top.

We found this recipe online years ago, and have long since lost the link to the source.

Update April 2007: Added honey as an alternate for the corn syrup.

We're off, once again

My SO and I are heading off for a week-and-a-half long trip to the east coast, our second trip of this break. The primary reason we're going back is to visit my mom (for an occasion to celebrate), but we'll also be visiting my SO's parents in Philadelphia.

I've got a few things cued up, so you can expect at least a couple of posts while I'm gone (no guarantees, though ... we might just gorge ourselves on cheesesteaks 24/7).

It's published!

My lab manual is now in print. I just ordered a copy for myself (that won't get here for at least a week), so right now I have no idea how it will look in person. It's a relief to have it done, but it's depressing to know that there are probably mistakes (since I didn't have enough time to polish it as much as I'd like). However, I'll be selling it only to my own students for at least the first year of publication, so I should have time to improve it.

Unfortunately you won't be seeing a link to the manual from here anytime soon, partially because of the limitation on sales to my own students, but also because it's published under my real name. Sorry.

Pharyngula has moved!

PZ Myers has moved to http://scienceblogs.com/pharyngula; you can read all about the details of his new site here and here.

The site is hosted by Seed, and while the new hosting agreement seems like a great deal for PZ, his host's terms & conditions (which apparently apply to PZ's work as well) seem a bit restrictive:

Except as expressly authorized by the Terms or on the Site, you may not copy, reproduce, distribute, republish, download, perform, display, post, transmit or otherwise use any of the Materials in any form or by any means, without the prior written permission of Seed Media or the respective copyright owner. Seed Media authorizes you to view and download the Materials only for personal, non-commercial use, provided that you keep intact all copyright and other proprietary notices contained in the original Materials. You may not modify or adapt the Materials in any way or otherwise use them for any public or commercial purposes.

Yikes! It sounds as though they don't even want people to post quotes from him.

[Update: It looks like Seed has changed its policy. Chris, who works with Seed, left this comment only a few hours after my original post.]

Why our prior homeowners are idiots, reasons 138 and 139

Reason 138:

My SO was awakened this morning by a lovely sound: that of our house falling apart.


Prior to 6:50am today, those shelf brackets were actually square with the wall, and supported a shelf and lots of clothes. Luckily (for me), I was already awake when the brackets decided that the wall was no longer the supportive, caring structure that it once was; unluckily (for my SO), this shelf was installed at the foot of our bed, in which my SO was still soundly sleeping. And yes, the shelves were installed by none other than our prior homeowners.

Reason 139:

We're doing a major reorganization of our garage this week, part of which entailed removing a 2'x4' section of peg board from a wall so we could move some cabinets (with the eventual goal of setting up a large garage organizer). When we removed the peg board, we found a little present:


How can one manage to install a peg board and not notice that there are car-care products still on the wall? (oh, wait, I know the answer to that ... I saw this house before our prior owners moved out)


Some owners find priceless antiques stored in their attics; we find Johnson's holiday car washing cream hidden away in our garage. Anyone have any idea what era these products date to?

New exercise plan

My SO and I now have a new exercise plan, which we've posted over on the gym. Hopefully it will give us the long-term motivation necessary to keep up exercising.

That's going to be it for today, as the lab manual needs to be in by Friday (when we leave for another trip).

Yikes!

Slashdot just linked to an article reporting that burned CD-Rs and CD-RWs have expected lifespans of only two to five years. The report has spawned lots of debates in the thread's comments (the article presents no data backing up the claim), but it does make me wonder if I should go re-burn my backups from five years ago.

Implications of the Hwang case for authorship in academia

Seoul National University released its final report (official English summary here) on the fabrication of results by discredited stem cell researcher Woo Suk Hwang. I'm not a molecular biologist, and am even further from being a specialist in stem cell research, so I'm going to refrain from attempting to summarize exactly what has happened biologically in this case. However, the case is interesting, so here's a short summary of the final report:

1) The results reported in Hwang's 2005 Science paper (Hwang WS, Roh SI, Lee BC, Kang SK, Kwon DK, et al. 2005. Patient-specific embryonic stem cells derived from human SCNT blastocysts. Science 308: 1777-1783) were completely fabricated:

The data in 2005 article including test results from DNA fingerprinting, photographs of teratoma, embryoid bodies, MHC-HLA isotype matches and karyotyping have all been fabricated. ... In conclusion, the research team of Professor Hwang does not possess patient-specific stem cell lines or any scientific bases for claiming having created one.

2) The results in Hwang's 2004 Science paper (Hwang WS, Ryu YJ, Park JH, Park ES, Lee EG, et al. 2004. Evidence of a pluripotent human embryonic stem cell line derived from a cloned blastocyst. Science 303: 1669-1674) were also entirely fabricated:

The claim in 2004 article that the DNA fingerprinting pattern of NT-1 and that of the donor A match perfectly was a clear false report. Given that none of the alleged NT-1 derived cells or tissues match the donor A, the committee concluded that NT-1 ES cell line reported in Science in 2004 is not an ES cell line derived from a cloned blastocyst. In addition, claims that photographs of cells in 2004 Science article are those of MizMedi ES cells have also been confirmed to be true. Therefore, the committee concluded that results described in 2004 Science article including DNA fingerprinting analyses and photographs of cells have also been fabricated.

3) The results in Hwang's 2005 Nature paper reporting on the cloning of a dog (Lee BC, Kim MK, Jang G, Oh HJ, Yuda F, et al. 2005. Dogs cloned from adult somatic cells. Nature 436: 641) were confirmed; the dog exists, and appears to have been cloned.

4) Not only did Hwang fabricate research, but it also appears that he used eggs donated by his junior researchers and technicians, opening questions about whether implicit or explicit coercion was involved:

Regarding the article in 2004, Professor Hwang claimed to have been unaware of the egg donation by the laboratory members. However, the graduate student who donated eggs informed the committee that the act of donation, while voluntary, was approved by Professor Hwang. Egg aspiration was carried out by Dr. Sung Il Roh on March 10 of 2003 at MizMedi Hospital, and notably, Professor Hwang accompanied the student to the hospital himself. In May of 2003, Professor Hwang's research team circulated a form asking consent for voluntary egg donation and collected signature from female technicians.

Science has a very good summary (free full-text) of how this fraud was uncovered by anonymous message board posters and journalists using somewhat unethical techniques.

One of the issues that this case brings up is how authorship on scientific papers is determined. Authorship is typically not determined by who writes the paper (though the person actually writing the text of the paper is typically an author). Instead, the list of authors is determined by who made significant contributions to the research. Often, the only contribution made by authors may have been financial or physical resources (getting grants or providing facilities), or a highly specialized technique that is relevant to only one small portion of the research (and thus the author may have no knowledge of the rest of the work in the paper). In fact, the list of authors on a paper can be determined before the research has even begun; this is often recommended so that it's clear to everyone who's getting the credit for the work (so three people don't argue at the end of the research that they should all be first author), and to encourage people to work together (the idea being that if you know you're going to be an author on a study, you'll work harder).

In theory all authors should review the final manuscript and have a say in what's written, but I have a hard time believing that papers with dozens of authors can have feedback from everyone incorporated into the paper, much less have everyone actually verify that the data were collected properly. Hwang's 2005 Science paper had 25 authors spread across multiple continents. Was it even possible that they could have verified the experimental results, especially given that one of the researchers was lying? And what happens to Hwang's 24 coauthors now that the paper has been shown to be fabricated?

Hwang is not alone in having large numbers of coauthors; the best example I know of is a landmark 2004 ocean fertilization study (Coale et al. 2004) that had 48 authors, which was then cited by another paper (Armbrust et al. 2004) that has 45 authors. Even a quick review of the Science issue Hwang's paper was published in shows that more than half of the research reports had at least five authors, and two (excluding Hwang's) had more than ten authors.

The reason why authorship is handed out so readily is that authorship is academic gold, especially in big-name publications like Science and Nature. Getting a paper in Science or Nature is a Very Big Deal; it gives you the ability to obtain funding (and get positions) you otherwise couldn't get. When there are such huge rewards for obtaining authorship, and no clear guidelines as to what constitutes a contribution sufficiently large enough to obtain authorship, it's no surprise that huge lists of authors are a reality.

Complicating the matter is that a lot of scientific writing is based on trust. To use myself an an example, all of my published papers have been coauthored with at least two other researchers, yet in all of the cases where I was the experimenter carrying out the research, I was the only one of the authors who actually saw all the raw data and analyzed it. The only thing my coauthors saw were the summary graphs I showed them, and me in the lab working hours upon hours at my experimental setups. I easily could have faked the graphs and statistics after collecting the data, and my coauthors would have had no way of knowing, short of re-analyzing tens of thousands of datapoints or redoing months of experiments (especially because, unlike Hwang, all of my experimental organisms were destroyed at the end of the study due to the data collection techniques involved). My coauthors all contributed significantly to the ideas in my papers, and thus deserved authorship, yet they had no realistic way of knowing whether I forged my data or not. So, should my coauthors be held accountable if it were found that I had forged the data?

One possible way to get around some of these issues would be to require authors to list exactly what they contributed to the paper. That way it would theoretically be clear who did what, and then if one portion of the research was found to be improperly conducted, it would be clear who should be held accountable.

Self-publishing a lab manual

About a year and a half ago, I started teaching a new lecture and lab course. I wrote most of my own labs for the course, and for the last few semesters I've been distributing the labs as handouts on my course website. This has been far from ideal, however, as the vast majority of students didn't print out the labs, and many failed to refer back to past labs, even when they were relevant to current content (as a side note, the lack of printing is probably partially my fault, as I always had extra copies of the day's lab in lab).

So, the time has finally come for me to publish my own lab manual. I looked into having the manual published by a professional science publisher, and while they were extremely willing to give me help (and many publishers came to my office to talk about the project), there were two major problems: price and flexibility. I was often quoted prices over $30 or $40 for my 250-page, black and white manual, which seemed somewhat steep (see below for comparisons). The largest problem, however, was flexibility: all the publishers would have required me to do a printing run of at least 200 or 300 copies, meaning that I wouldn't have been able to revise the manual for at least two years. Considering that I haven't had time to perfect every single lab, and there're still a few labs I'm working on writing my own versions of, I just couldn't commit to that size of a run.

So, instead of going with a professional science publisher, I'm self-publishing my lab manual. There are a number of companies that will do print on demand (POD) publishing; both Cafepress and Lulu will publish 8.5" x 11" spiral-bound black and white books. The price and minimum run size of these POD companies is near perfect: both will print the book for less than $17 per copy (students can buy the book directly through the POD company's website), and neither has a minimum run size or up-front fee.

There are some definite downsides to self-publishing a manual, however. The professional publishers all showed me huge databases of images that I could draw from; by self-publishing I'm now responsible for clearing all copyrights for all images (and other content) in the manual. Thankfully I don't need too many images, but even so, in the past two weeks I've sent out dozens of e-mails requesting permission to use various images in the manual. A relatively minor problem is that none of the POD publishers I've seen have an option to have perforated pages, which will make end-of-lab worksheets somewhat more annoying to collect (they'll have to be torn out of the manual). I'm also now responsible for all formatting of the manuscript - the only thing the POD publishers do is take a Word file and print it as-is. This means that I've just taken a crash course in publishing style guides and how to use Word professionally (thank you Google!)

Formatting the manuscript has, so far, been the most time-consuming task (other than spending the last two years writing the labs). Even though I've used Word regularly for more than ten years, I can't believe how much I didn't know. I've now learned how to use styles, the outline view, section breaks (which, for instance, let you always start a chapter on an odd page), bookmarks and cross-references (which, when combined, dynamically update links such as "see page X"), the outline view, and automatically generated tables of contents. Probably the most useful of these new skills was an understanding of styles: they've allowed me to reformat my 20+ labs into a format that is consistent throughout the book, yet is easily changeable. For instance, now that I have styles set up, I can change the font (or paragraph spacing, or bullet style, or whatever) of all the body text in my 200+ page document without changing anything about my heading, captions, or other text styles. It's amazingly convenient.

Here are a few of the many pages I've used to study up on Word; I highly recommend them:

Yes, You Can Use Microsoft Word to Set Type That Looks Professional.

Microsoft guide to styles, which links to how to apply a style and how to format a style.

The above led to how to create a template, a very useful guide to making and formatting a good Word template to start writing.

Using outline view - assuming you're using headings properly (which I am now!), learning how to use this view will save you lots and lots of time.

How to create a table of contents.

A short note on how to prevent sections of text from splitting across pages.

A summary of how to format front matter differently from the rest of the book.

Two summaries of how to do page numbering in Word.

Cafe Press guide to front matter - a great guide to what goes where.