The wireless tour of Vancouver

I'm now in Vancouver, and am finally back on the net, albeit temporarily. I'm writing to you from Take 5, a coffee shop in downtown Vancouver that's kind enough to offer free wireless net access.

Getting said wireless net access has been harder than I initially anticipated. Before I left home I downloaded some pages from Wi-Fi-FreeSpot, and hoped to be able to find some in the cities we were traveling through. Unfortunately we haven't found any before today because either there weren't any spots listed, the spots were too far away from where we were, or we were too busy touring to look for places. Also, I was on a relatively undeveloped island for much of the past week, which didn't help anything.

So, today my SO and I decided to hunt out some free net access. We found one coffee shop on the map and drove across town to find it. Somewhere along the line the 245 address turned into 345 in our heads, and thus we arrived at a check cashing place instead of a coffee shop. There was a library nearby so we wandered over to there, only to discover it was closed on Mondays. Upon driving away unsatisfied we saw the coffee shop at 245, and stopped in. We spent about 45 minutes fiddling with settings and talking to the helpful barristas, but alas all we got out of that coffee shop was a very good iced chai.

We then headed downtown, where there were two locations near each other. We couldn't access the first of the two wifi points, but were able to access the second. I would have loved to see a MRI of our brains, as I'm sure the pleasure centers lit up the moment we saw we were online :)

This searching has given us a very nice introduction to Vancouver. After driving around we've concluded that this is an amazingly diverse city. Along one street (Broadway) we found the following types of restaurants all within 2-3 miles: Japanese, Szechuan, Mandarin, Vietnamese, Thai, Korean, Malaysian, Greek, Indian, Italian, American, southern BBQ, Afghan, generic middle eastern (falafels etc.), a horde of coffee shops, and your usual fast food places. And we only have three days to try them all!

I just found out that this coffee shop is closing within the hour, so I'm going to post this, send off a much delayed e-mail to a friend, and then see if I can get some pictures online using Blogger's new photo hosting tool Hello.

Leaving Victoria for Nanaimo

Just a quick post as we leave our B&B here in Victoria for a drive up to Nanaimo where we'll meet some colleagues from my campus and will travel with them for about a week (until next Saturday). Yesterday we traveled to Butchart Gardens which was quite enjoyable even though it softly rained on us the entire time. In the evening we relaxed in our supremely comfortable room and read to the sound of falling rain.

We were planning on heading to Vancouver next Saturday, but on Qov's suggestion have decided to come back to Victoria for a day so we can see the provincial museum before heading to Vancouver for a few days.

In Victoria, BC

My SO and I arrived in Victoria, BC today after taking the Coho ferry from Port Angeles, Washington. We're staying at a bed and breakfast near downtown tonight and tomorrow night before heading up north on the island to meet up with my colleagues.

We were both happy to find that our B&B has a computer hooked up to the net, but were sad to discover that it's only a dial-up. That, combined with the lack of photo-editing software on our laptop, means that no pictures from the drive will be coming up soon, sorry :(

While most of the past few days have been spent driving, tonight we got into town early enough to enjoy a leisurely dinner out. Our B&B hosts suggested a few seafood restaurants, and we chose the Wharfside Eatery & Decks. I had some sea bass that was some of the best fish I've ever had, and my SO had some very tasty scallops. It was a romantic candlelit dinner on the waterfront, complete with the sun setting during dinner, a very nice beginning to our time here in Canada. We found it odd, however, that the sun set after 9:30 pm.

p.s. Thanks to everyone who commented on my going-away post; it was very nice to open up my blog tonight and read the comments :) I can't wait to get out tomorrow and explore.

Leaving for Canada

I'm leaving today for a college-related trip to Vancouver Island, Canada. My SO and I are driving up, will be spending approximately a week with a few other colleagues from my campus, and then will spend some time in the Pacific Northwest enjoying our first real vacation (not to visit family members or each other) in longer than either of us would care to remember. We plan on staying in at least one bed and breakfast in Victoria, may do the same in Vancouver and/or the Olympic Peninsula area (though we have no specific plans yet), and just hope to casually explore the area and relax for a week or two.

I will have a borrowed laptop (that has a wireless net card) with me, and I'll try to post notes up every now and then throughout the trip, but I have no idea how much success I'll have (I'm new to this wireless thing; chalk me up as a desktop addict). Thus don't expect much until after I get back from Canada in late June or early July (and if you do see things in the next few weeks they're likely to be very travel oriented).

I apologize for the long absence. I hope everyone has a great few weeks!

p.s. as a final note, is it a sign that you're a geek going on vacation when you bring along more books and science magazines than you can possibly read, even if you spend all day every day reading?

Yard update and chlorophyll synthesis

Yesterday my SO and I finally finished work on our newly created planting bed. We'd planted roses and bulbs earlier, but to finish up we added some edging, put in a new watering timer, and spread out some mulch. The bed is really nice now, but it doesn't look like we've put nearly the amount of time and sweat into it that we have.

We have been pleasantly surprised by the plants' progress, as we found our first rose flower bud and amaryllis flower bud coming up yesterday. Of course we promptly cut off the rose buds after taking a picture because the plants are far too young to be doing that sort of thing.



Those with good memories will remember that we only planted the bulbs a few days ago, and will probably wonder how the amaryllis was able to grow so fast. We'd been storing the bulbs in a cool, dark closet, and the amaryllis had started sending out leaves in the closet before planting day. The amaryllis leaves were pure white when we planted them; there wasn't even a hint of green in them. Then, the next day we could see hints of red and green in the leaves, and on the second day after planting the leaves were solid green.

This color change occurred because light is a critical component for the reactions involved in chlorophyll synthesis. In the absence of light plants will synthesize precursors of chlorophyll, but they cannot make the actual molecule. Thus, when the amaryllis was growing in the dark closet its leaves were filled with precursors of chlorophyll, but it couldn't turn those precursors into chlorophyll because there was no light. When we planted the bulbs light became available and the leaves were finally able to synthesize chlorophyll.

I apologize for not having the names of the precursors or details of the synthetic pathway; I had intended to look them up before posting but my botany supplies are in the office and I'm leaving for a trip tomorrow and wanted to get this up before heading off.

Tray Table Advertising

Flying back from Dallas to Las Vegas last week on America West we were surprised to find the following department store advertisements on the tray tables (I've blurred any identifying text):



So, apparently while I'm flying I want to look at either shoes or a pseudo-hunk lounging around. I actually first saw this style of ad on America West a few months ago when the tray tables in my row all had car ads on them, but I didn't have a camera with me to snap a picture.

Texas Woofus: mystery solved

On my recent trip to Dallas I visited Fair Park along with Semantic Compositions, our SOs, and another friend. We went to the park hoping to visit the gardens there, but upon arriving we found that the gardens were closed. My SO quickly discovered that the nearby aquarium was open, but Semantic Compositions and Mrs. SC nixed that idea (darn non-biologists not appreciating nature), so we looked for the nearest directory.

On that directory we found a list of "Special Interest Points":

Since none of us had any clue what a Texas Woofus was, this meant it had to be something cool and thus we set out to find it. First up was to find it on the map:

Of course the Woofus was across the park from where we were, but we were sure the Woofus would be well work the trek. On the way to the Woofus we passed the Cotton Bowl stadium, what looked like an abandoned amusement park, and the portion of Fair Park every tourist longs to see: the State Fair of Texas Administrative Offices.

When we arrived at the location specified on the map all we found was a very plain-looking building labeled "swine".



We figured that most Texans would know to call a swine building a swine building, so we kept looking. We found another map, confirmed we were in the right place, and then walked around the swine building again, but there was still no Woofus. We eventually gave up and headed off to the Texas Hall of State, and SC and I swore to discover later what a Woofus was.

This morning I'm proud to announce that I finally discovered what the Texas Woofus is: it's a statue that we walked past at least two times (so much for our scientific powers of observation). In fact it is barely visible on the left side of the picture above:


The Fair Park art and architecture fact sheet (link is a PDF) has more information:

"The Woofus, a combination of six classic Texas animals, sits outside the Swine Building atop a 16-foolt [sic] pedestal and was originally created for the 1936 Texas Centennial Exposition by sculptor Lawrence Tenney Stevens but disappeared shortly thereafter. It has a sheep's head, a stallion's neck, a hog's body, turkey feathers and duck wings. The "crowning" glory of the piece is a set of ten-foot wide Texas longhorns gilded with chromium with a crown perched between them and a Mexican blanket draped around his shoulders. The Woofus was returned home in September of 2003 thanks to the efforts of Friends of Fair Park and the State Fair of Texas."

The mystery of what a Texas Woofus is can now be laid to rest. Check this site in the future for more equally compelling pieces of detective work from Radagast, Semantic Compositions, and team!

Recent Food

It's been a very food-filled past few days, as my SO and I have finally had time to do some good cooking. I just started some chicken etoufee, which is now simmering on the stove and tempting both of our noses with the scents of browned chicken, onions, garlic, peppers, and cajun spices all in a dark roux. When it's done in half an hour I'll be ecstatic.

In the past few days we've also had some other great food, including some of my mom's classic crab dip on fresh ciabatta and homemade chocolate chip cookies. The cookies are some of the best I've had, as each cookie is made from a heaping 1/4 cup of dough and is soft and chewy throughout, even after baking. We also made a good bacon tomato pasta sauce a few days ago, though it wasn't anything unique.

Both my SO and I enjoy cooking, and when I'm off in the summer we will often spend hours in the kitchen. If I had a specialty it'd be baking: breads, muffins, biscuits, scones, etc., and my SO's specialty is making white sauces, sweets, and improvisational cooking based on what we've got around. We almost never cook alone, though, and I cherish our time together in the kitchen.

Since we enjoy cooking so much we're both baffled by folks who don't spend time cooking; the rewards of cooking a good meal are vastly worth the time.

Well the timer has gone off and it's time for me to get back to the chicken etoufee (my SO just picked some scallions from the yard and is chopping them as I type).

Congratulations!

I wanted to send out some congratulations to a friend who just ran his very first marathon today in San Diego. Considering that I could probably run, oh, maybe 1/100th of a marathon before needing a breather, I'm quite impressed!

[Update 6/8/04: I just learned that his time was 4 hours and 40 minutes.]

Variability in plagiarism

Pharyngula has an excellent response to a case of plagiarism in which a student is threatening to sue his university because he's been punished for plagiarism. I'm not surprised by this student's response (some of the plagiarizers I've caught have been quite defiant), but am stunned that some people have found grains of truth in the student's argument and believe the student shouldn't be expelled.

The student is claiming that he was never told plagiarism was wrong, and that he'd gotten away with it in the past so he should be allowed to get away with it now. Pharyngula's major points are that ignorance of the law is no excuse, and that getting away with a crime in the past does not mean that you can commit the same crime in the future. To carry the crime analogy further, I'd add that if students are found to have plagiarized an assignment then it makes perfect sense to reexamine all of the student's prior work for plagiarism as well, just as the police would check to see if a newly caught bank robber's profile fit any previously unsolved bank robberies.

One of the points that I've seen missing from many discussions on plagiarism is just how varied plagiarism can be. Not all plagiarism is capital-P Plagiarism wherein an entire paper or large fraction thereof has been copied from the net or a book. Among the cases of plagiarism I've caught in a few years of teaching biology, almost every one has been different in scale or style from the others. I can think of two scales for ranking plagiarism severity that can independently vary: the degree to which the student has cited their work, and the degree to which students have used other people's work.

Degree of citation (assuming word-for-word plagiarism):

1. No literature cited section, in-text citations, or quotes around the copied text.
   
2. Literature cited section at the end of the text that doesn't contain the work that has been plagiarized from, with no in-text citations or quotes around the copied text.
   
3. Literature cited section at the end of the text that possibly contains the work that has been plagiarized from; the work may be cited incorrectly or too vaguely to be identified (e.g. the root homepage of a university instead of a faculty member's research paper), with no in-text citations or quotes around the copied text.
   
4. Literature cited section at the end of the text that does contain the work that has been plagiarized from, but no in-text citations or quotes around the copied text
   
5. Literature cited section with the proper reference and an in-text citation by the plagiarized portion, but no quotes around any of the copied text.
   
6. Literature cited section with the proper reference and an in-text citation including quotes around some of the copied text, but with portions of the copied text not in quotes.
   
7. Literature cited section with the proper reference and an in-text citation including quotes around all copied text (not plagiarism).
   

Amount of copied material:

1. Entire assignment is copied.
   
2. Large fraction of the assignment is copied, but the student has written some interlinking portions.
   
3. Moderate amount of the assignment is copied, with a moderate amount of original student work.
   
4. Small amount of the assignment is copied, possibly only a sentence or two, with the majority being original student work.
   
5. Nothing has been copied (not plagiarism).
   

Combining both axes means that there are at least 24 different ways that students can plagiarize, and I've probably left out a number of variants. Note that neither of these scales properly takes into account plagiarism of ideas but not wording, which is significantly more difficult to detect with absolute certainty, or the variability in source materials used for the plagiarism.

I've observed cases of plagiarism that vary widely on both of these axes: I've had students take multiple quotes from a source and cite them properly, only to take one or two sentences from the same source and not quote them, and I've had other students turn in papers that are almost entirely copied from a few websites that are not cited. While all of these cases (1-6 and A-D in the lists) are clearly plagiarism, I'm not sure they deserve the same punishment, especially since the milder cases (e.g. 6D) could easily be accidental, caused by nothing more than sleep deprivation and stress. This variation is one reason why I don't like most zero-tolerance policies regarding plagiarism (e.g. automatic F in the course or expulsion), even though I despise plagiarism.

For the most minor cases, a 6D and a one-sentence 5D, I reduce the paper's grade by a goodly number of points and give the student a stern warning. For all other cases my minimum punishment is a 0 on the assignment, the inability to receive an A in the course, and a referral to the dean. This referral ensures that the plagiarism is permanently noted in the student's disciplinary record, and the dean may give further sanctions if desired. I also give myself leeway to be more strict for severe forms of plagiarism; this past semester I caught a 1C student, and in that case I failed the student from the course. I'm relatively comfortable giving my students severe punishments for plagiarism since I provide a lot of guidance on literature citation and avoiding plagiarism in all my classes, including lecturing on the topic, distributing two separate handouts on plagiairsm, and including a section on academic dishonesty in my syllabus.

I've also discovered that plagiarism is not easy to identify, or at least it's not easy for me to identify. I first started electronically scanning for plagiarism three years ago when I'd gotten a crop of about 50 student papers, and while grading them noticed that one was pretty suspicious (not telling me things I'd asked for in the assignment, using unusually advanced terminology, etc.). I manually scanned the paper in, used optical character recognition (OCR) software to convert the scans to text files, and subsequently found that the paper had been almost entirely plagiarized from one website. After finding that case I decided to scan in and OCR every paper from that batch, and discovered that ~30% of the papers contained some form of word-for-word copying plagiarism. I'd read all of those papers, and hadn't suspected that anything was awry in most of them. Thus either I'm especially clueless (not a hypothesis to discount quickly), or plagiarism is harder to detect than one would otherwise think.

To this day I do the same thing, grading papers before I've scanned them for plagiarism, and I'm still surprised to find cases of plagiarism where I'd already read the paper and hadn't suspected anything. Afterwards, I do often spot differences in formatting or writing style between the plagiarized and non-plagiarized portions of the text, but detecting those differences while grading a pile of 100+ papers can be challenging.

Given the low numbers of plagiarism cases that I hear most other faculty reporting (one or two a year, if that), I suspect that many cases are going undetected. For the past four semesters I've made a huge deal about plagiarism in my classes, including explicitly telling students that I will be electronically scanning their papers for plagiarism, and I've still discovered more than 20 cases (even though I teach biology and assign only two relatively short writing projects a semester).

Night planting and car repairs

It's been a busy day of working around the house and shopping at the IKEA sale, but two things stand out as being mildly interesting.

1) Night Planting: My SO and I have discovered that gardening at night is quite enjoyable; it's wonderfully cool, there's no worry about getting sunburned, and as long as we have our halogen work lamp on we can see just fine. We just came in an hour ago after planting approximately 50 bulbish things in and around our new rose bed. We planted a selection of cannas, calla lilies, ranunculus, dahlias, and amaryllis. We're imagine this is the wrong time of year to plant them, but oh well, that's what one year plant guarantees are for.

For those botanically minded folks out there, most of what we planted are not true bulbs; in the list above the only one is amaryllis. True bulbs are a plant bud that consists of a small stem and a number of leaves. Onions are common example; each layer of the onion is actually a separate leaf. Dahlias and cannas are tuberous roots (root tissue modified to store nutrients), ranunculus are tubers (swollen underground stem bases), and callas are rhizomes (underground horizontal stems; information primarily from Sunset's Western Garden Handbook).

2) Car Repairs: As I mentioned earlier, we were frantically trying to get our "travel" car repaired before our recent trip to Dallas. We got the car back from the repair shop on Thursday afternoon of last week, took it in for a quick oil change at an EZ Lube, and were planning to drive it for hours through the desert later that night. Unfortunately, on the way home from the oil change place my SO noticed that the engine was getting hotter than normal and had started smoking, but after parking and opening the hood we couldn't figure out where the smoke had been coming from. With time running short, we decided to take our other car (which only I can drive because it's a stick shift) on the trip.

After getting back from Dallas we started the "repaired" car up and looked for leaks and smoking, but didn't see any. This morning we drove the car to the repair shop to figure out what was wrong, and the engine started smoking about half a mile away from the shop. We opened the hood, called out the mechanic, and after about 30 seconds he found the problem: the dolts at the EZ Lube had forgotten to tighten the radiator cap. We felt pretty dumb for not having found it, but at least it seems like no major damage was done.

Window installation hiccups

Yesterday I woke up at 7:30 am to finish up some drywall removal in the master bathroom before our contractor's team arrived at 9:30 am to start installing new windows. We'd confirmed, last week, with our window company (1st Windows) that the windows would be delivered yesterday, and our contractor called the night before and again confirmed that they'd be delivered yesterday, even getting a time estimate of 1-3 pm. My SO and I were psyched as wood was cut and drywall was ripped out; progress was finally being made and in a few days we'd have new windows. Then, if all went well, next week the bathroom would be drywalled.

The new framing was largely in place for all three windows when, around 3 pm, we got a call from 1st Windows saying that our windows were still in Oregon and would not be delivered until at least the eighth of this month. The company said they'd try to see if they could speed things up and that they'd get back to me later, but I still hadn't heard anything by noon today. I called the company today at noon and they didn't have any clear answers; they've supposedly talked to the window manufacturer and they're trying to see if a local plant could make the windows, but they have nothing certain yet. Needless to say I am not happy with 1st Windows and Milgard (the window manufacturer) right now.

The workers have patched things up so there are no holes in the walls (the old windows had not been removed yet, but some siding had been), and we're now in limbo while we wait to hear when our windows will be delivered. Unfortunately my SO and I have a multi-week trip to the Pacific Northwest and Canada starting around the ninth of this month, so this delivery problem could end up delaying our window installation by more than a month, and might also cause problems for our trip because we have to be home for the window delivery.

[Update Monday June 7, 2004 (5:30 pm): We have heard nothing from 1st Windows since this post.]

Those shoes are comin' off

While on my recent trip to Dallas for a friend's wedding my SO and I had the pleasure of being screened by TSA employees twice. My SO owns a pair of black John Deere work boots that look like they could have a steel toe or metal shank in them, but they don't. The boots have gone through metal detectors without setting off alarms at least three times, and my SO has never set off the alarm while wearing the boots. Even though my SO informs screeners of this, the screeners usually insist that the boots be removed before going through the metal detector. This has always riled up our blood, since the TSA says that removing shoes is optional but the screeners never put it that way.

While getting screened in Las Vegas this weekend my SO was, once again, asked to remove the boots. When my SO politely responded that the boots are able to make it through the metal detector just fine, the security agent said forcefully, "Those shoes are comin' off." The boots came off, and we went on our flight without problem. We did both decide, however, that it would be fascinating to test what would happen if we didn't remove our shoes. In case you're curious, the reason my SO and I wear boots on flights is so that they don't take up half the volume of our suitcase, instead choosing to pack our much smaller biologist-issue Birkenstocks.

Two days later in the Dallas airport we had an opportunity to run our test. My SO, still wearing the same boots, moved quickly through the screening point and was not asked to remove the boots. No alarms went off and my SO exited the security area wearing the boots without problem. My boots, however, caught the screener's attention. My boots are well-worn brown leather Timberland hiking boots that usually don't attract the attention of screeners; their sole is a bit thicker than normal tennis shoes, but nobody would ever confuse them with heavy steel-toed work boots.

What follows is the entire exchange at the security station. To give some background, before approaching the screening station I took all items out of my pockets and put them into my backpack. The screener asked the person in front of me to remove his belt, and upon seeing this I also removed my belt, in front of the screener, and put it into a basket to be X-rayed. The interaction starts as I remove my belt.

SECURITY 1: "We suggest that you take off your shoes, sir."
RADAGAST: "Why?"
SECURITY 1: "They'll set off the detector."
RADAGAST (politely): "They don't set off the metal detector when I have no other metal on me."
I observe that the metal detector is not blocked, so I turn and slowly walk through it.
METAL DETECTOR: "..."
Security 2, who was watching the earlier exchange, moves into my path about a foot after I've gone through the metal detector and points to a roped off area just past the metal detector, which a friend aptly named the "penalty box." Security 2 says nothing at first, only speaking after observing that I understood his clear and concise directions and have started moving towards the penalty box.
SECURITY 2: "Stay there."
Security 2 walks to the end of the baggage screening ramp (about 10 feet away).
SECURITY 2: "Which are your bags?"
RADAGAST: "The backpack, and the brown belt."
Security 2 grabs the backpack, and holds up a belt.
SECURITY 2: "This the belt?"
RADAGAST (never having realized how difficult it is to identify a belt from 10 feet away): "Uhh."
SECURITY 2: "There's a lot of belts." (Well, duh. Guess that happens when you ask people to remove them.)
Security 2 makes no attempt to bring the belt closer, but does hold up another belt which looks vaguely like mine.
RADAGAST: "Yeah, that's it."
Security 2 moves my bag and belt to another table, then walks back next to me.
SECURITY 2: "Wait here."
Security 2 and I wait in the penalty box for about a minute while the two people who were screened in front of me finish assembling themselves.
RADAGAST: "Did I set off the metal detector?"
SECURITY 2: "No."
I was going to follow up, but at that time a third security agent approached from the screening area.
SECURITY 3: "Sit in that chair."
I sit, smiling with the knowledge that this entire exchange will be going on my blog within 24 hours of my return (OK, so it ended up being 48 hours).
SECURITY 3: "Raise a foot."
I raise a foot, after deciding that jumping about 1/3 of a meter into the air is probably not what Security 3 desires. Security 3 proceeds to wave his metal-detecting wand at my shoe.
METAL-DETECTING WAND, when placed near shoe: "Beep."
SECURITY 3: "Remove your shoes."
I remove my shoes, taking no pains to hurry. Security 3 takes my shoes and puts them in a basket for the X-ray machine, after which he returns to my chair.
SECURITY 3: "Please raise a foot."
I lift a foot and watch as Security 3 proceeds to wand the entire foot, then lift my other foot as Security 3 wands that foot as well.
SECURITY 3: "Please stand up. Face your bag."
I do so.
SECURITY 3: "Hold your arms out."
Security 3 proceeds to wand me on all sides, starting at the head and traveling down my right side. He then proceeds to feel me up with the wand between my legs, and continues wanding my left side. Once finished with my side, he asks me to turn and wands my back and then my front.
METAL-DETECTING WAND, when placed over my non-belted waist: "Beep"
RADAGAST: "That's odd." (Especially odd since I have no metal there other than a small zipper, and the detector wasn't going off over the zipper. I decide that I must have an alien implant in my abdomen.)
Security 3 takes the opportunity to feel me up once again, this time fingering my abdomen. Apparently he doesn't find the alien probe and stops his search.
RADAGAST (while being felt-up): "Why was I searched?"
SECURITY 3: "You set off the alarm."
RADAGAST: "I did not."
SECURITY 3: "Oh."
SECURITY 3: "For security reasons we cannot discuss passenger screening protocols."
I continue politely looking at Security 3, making sure the silence at the end of Security 3's last statement is as awkward as possible.
SECURITY 3: "But, in reality, we weren't wanding anyone and you were the next one in line."
Finding that the screening is over I assemble myself with as little haste as possible and then leave the screening area. I proceed to find a seat and jot down notes on the back of the paper boarding pass holder for the next 10 minutes.

While the sample size is obviously low (n=1), it seems likely that the only reason for my supplemental screening was that I defied an "optional" request of the screeners. The explanations I was given for the additional screening were both bogus: I know for a fact that I didn't set off the alarm, and considering that I had to wait for two other people to complete their wanding before I was wanded, it seems relatively obvious that I wasn't picked solely because the screeners were bored. There was no indication on my boarding pass that I was to be screened more carefully, and security agents 1, 2, and 3 never saw my boarding pass or communicated with the boarding pass screener in any way that I saw. Certainly this could have been a "random" check, but I'll never know if that was the case or not.

The TSA "shoe screening policy" makes it clear that removing shoes is optional:

"Passengers are not required to take off their shoes before going through metal detectors. However, if your shoes set off the metal detector, you will undergo secondary screening until the screener can locate the source of the alarm. If you know your shoes contain metal, you may voluntarily take them off, place them in a bin, and allow them to be x-rayed."

My SO has been ordered numerous times to remove boots, a friend on another flight to Dallas from Vegas over the weekend was told that if he set off the alarm after refusing to remove his sneakers he wouldn't be allowed to fly (he removed his shoes), and when I refused to remove my shoes during this screening I was immediately selected for "secondary screening", which included shoe removal. The TSA claims that shoe removal is voluntary, but they clearly have the power to arbitrarily select individual people and force them to go through additional screening, including taking their shoes off, even if they have not set off the metal detector.

As it is, what we have are policies that are arbitrarily and inconsistently applied by people who have total power over passengers with minimal oversight. People comply with these annoying and demeaning screening procedures without protest out of fear that they'll miss their flight, be screened more thoroughly for acting "suspiciously", be molested by screeners, or even be arrested. This hardly seems like a fair and just security policy.

I could support strict screening procedures if they were effective in preventing weapons from getting onto planes. However, our current screening protocols regularly fail to find the most obvious of the items they're searching for, as detailed in this March 2002 CNN report,

"In hundreds of undercover tests conducted between November and February [2001-2002], security screeners missed 70 percent of knives, 60 percent of simulated explosive devices, and 30 percent of guns. Overall, screeners failed 48 percent of the time."

I will close with the immortal words of PZ Meyers that rang through my head as I was being screened: "I shall splutter about it on a weblog. That'll teach 'em."

Tangled Bank #4

The fourth tangled bank post is up at De Rerum Natura. I'd also like to send a hearty thanks to Reed for linking to my recent plagiarism posts along with Tangled Bank 4.

Grading and construction surprises

Today was supposed to be a relaxing day of wrapping up a few loose grading ends at school and then checking to make sure the window installer was coming on Friday. Unfortunately it turns out that my lecture assistant at school had mis-entered three different assignments' grades, and thus I had to help her manually go back over all the papers. We got everything straightened out by the end of the day, however, so I'm now officially done with the spring semester. Yipee.

Then, after getting home, the window installer called and said that his crew would be showing up tomorrow at 9am to start work. Normally a contractor showing up early would be great, but we'd planned on spending the next two days cleaning out the rooms they're going to be working in, so we got to do that tonight (in lieu of, say, writing blog posts about our travels). The contractor also said that while getting the permit the city mandated some changes to the job, so our bedroom window will not be able to be in the position we'd wanted. We were hoping to expand the window one foot to both the left and right, but the city apparently says that the window is too close to the corner of the house and thus we can expand it in only one direction (away from the corner). There's enough room to work with, but unfortunately this means that a part of the window will likely be behind a door. Oh well.

I'm back

I got back from my trip to a friend's wedding in Dallas via Las Vegas this morning at 4am. I'll post more details about the trip soon, but first have to finish up some grading loose ends at school and make sure everything is on schedule for construction this week.

Wrapping up the semester

It's been a very hectic week here as I wrap up the semester. I gave my final exam in lecture yesterday, and spent most of last night and this morning grading the 270+ pages of answers, but I'm happy to say that I've finished grading it. My cortisol levels probably dropped by half after marking the last exam this morning. If you ever have colleagues tell you that it's impossible to give short answer tests in large lectures (say ~180 students to start, ~135 left), I hereby vouch that it's possible. Granted, only 30% of the final exam was short answer, but hey, it's better than nothing.

I've also had to get all my knowledge check and participation grades added up, as well as finishing grading all my student papers. The participation grading has been frustrating as it looks the program didn't receive ~10% of the responses from most students; I'll write a much more detailed post on that once I have time. The worst time suck has been the plagiarism reporting. In the last few days I've had to confront each suspected plagiarizer and file official reports with the dean. A back of the envelope calculation showed that yesterday I spent at least 7 hours working on filing plagiarism reports, and I'm still barely half done (7 filed, 5 to go).

This wouldn't be so stressful if I didn't have to leave early Friday morning (1 am) to attend a friend's wedding out of town, so I need to finish everything by tomorrow night. Add to all of this that the car we're driving to the wedding is currently in for repairs, and we've got a busy week.

I apologize for the lack of thoughtful posts; hopefully I'll be able to write more of those after the wedding.

Scratch that.

I have NOW found the stupidest plagiarism ever: another student turned in four of my in-class response system questions as their extra credit assignment.

Stupidest. Plagiarism. Ever.

I've spent most of the evening grading papers, and have found several more instances of plagiarism, including three students who plagiarized their final paper.

Then I started grading extra credit assignments. The assignment was simple: write four test questions on any topic we covered in class. The only caveat was that the questions couldn't be term recognition or definition questions, and the entire thing was worth a whopping four points, less than 1% of the final grade.

I was grumpily reading over the various questions when I came across the paper of one of my more verbally challenged students. Imagine my surprise, then, when I discovered that the questions were beautifully written using terminology that even I was unfamiliar with. After a bit of googling I found what I had suspected: the student had copied the four questions off of three exams that were posted on the net.

(insert head shaking here)

To make matters worse (for the student), after finding this plagiarism I realized that the same student's final project had also been plagiarized, and this extra credit had been turned in on the very same day that I talked to the student about the prior plagiarism.

This student will get no credit for either of the two assignments, and will have two separate plagiarism reports on their permanent academic record. I'll also request that the dean give the student a disciplinary F in the course (which cannot be erased by retaking the course), and I may ask for additional sanctions, possibly including suspension from the college.

All for a measly four points.

Note: In case you were wondering, I'm grumpy because I have to file 11 plagiarism reports with my dean by the end of the week, I've been grading for nearly a week straight, and I'm way too tired right now.

Note 2: As a shoutout to Semantic Compositions, the title of this post is a snowclone: "Xest. Y. Ever." I've done exactly no research on this, but from what I know it traces back to the Comic Book Guy from The Simpsons saying "Worst. Episode. Ever."

Electronic communication

I have 3 hours of office hours on Mondays, and with my lecture final exam tomorrow afternoon I figured I'd be bombarded with student queries. I was swamped, but not in the way most of my colleagues would expect. I've only had three students drop by my office today, one of those had to pick up a CD and the other two came as a pair. However, in the past three hours I've responded to 17 student e-mails and had IM (instant messenger) conversations with five different students. The queries ranged from the panicked "what is going to be on the exam?" style to detailed lists of questions that had obviously been prepared only after much careful studying.

Given that I'm teaching at a community college with no on-campus housing these numbers aren't surprising; most students only come to campus when they absolutely have to. I'd also guess that numbers like these are probably very common for readers of this blog. What's more surprising to me is that the faculty at my campus don't reach out more to our students using electronic communication. I don't know of anyone else on my campus using IMs to communicate with students (not that I've asked everybody), and a number of our faculty still either don't use e-mail or don't give their e-mail addresses to their students. I'm rather baffled by the lack of use, since I find electronic communication to be both convenient and very helpful pedagogically, and if nothing else I'm sure that these 20+ students wouldn't all have stopped by my office this afternoon.

And now that my electronic communication is done for the day, it's time to get back to grading.

In-class response system evaluation data

As promised, last week I asked my students what they thought of the in-class response system that we've been using this semester (EduCue's PRS system). I've previously discussed the positives and negatives of the system, as well as how I've been using the system in class. Here are the data:

How much did you like having the PRS transmitters in this class?

Liked them a lot	51%
Somewhat liked them	35%
Neutral	6%
Somewhat disliked them	4%
Disliked them a lot	4%

If you had a choice, would you have preferred this class use or not use the PRS system?

Greatly prefer the class with the transmitters	55%
Somewhat prefer the class with the transmitters	23%
Neutral – either way is fine	15%
Somewhat prefer the class without the transmitters	3%
Greatly prefer the class without the transmitters	4%

Do you feel that the in-class response system helped you understand the topics covered in this class?

Helped a lot	56%
Helped a little	31%
It didn't help or hurt	11%
Hindered learning a little	1%
Hindered learning a lot	1%

Did the in-class response system help you stay involved/interested/awake in lecture?

Helped a lot	56%
Helped a little	32%
It didn't help or hurt	7%
Hindered a little	3%
Hindered a lot	2%

Would you like other instructors to use the PRS system? For this question, assume that you would not have to buy a new transmitter or pay anything more.

I definitely want other instructors to use the system	59%
I somewhat want other instructors to use the system	20%
I’m neutral – no preference	16%
I somewhat don’t want other instructors to use the system	2%
I definitely don’t want other instructors to use the system	3%

Would you like other instructors to use the PRS system? For this question, assume that you would have to buy a new transmitter or pay an additional registration fee.

I definitely want other instructors to use the system	10%
I somewhat want other instructors to use the system	18%
I’m neutral – no preference	13%
I somewhat don’t want other instructors to use the system	13%
I definitely don’t want other instructors to use the system	45%

The survey was done in class this past Tuesday using the PRS system, though I ensured every student without a transmitter was able to turn in responses as well. The survey was conducted in the middle of a lecture and was completely anonymous; students saw me select the "anonymous, do not record individual IDs" feature on-screen before starting the survey and were invited to trade transmitters with their neighbors if they desired. Sample sizes ranged from 103-112 students answering each question.

I'm very pleased with these results; I could hardly have hoped for better, especially considering this is the first semester I've used the units. To summarize a few of the highlights:

• 86% of students liked that the class used the in-class response system
  
• 79% of students would prefer that the class use the transmitters, a sizeable number considering that they each spent $15-$40 to acquire them.
  
• 88% of students felt the system helped them learn the material; the same number also felt the system helped them pay attention in class better. I'm only half-joking when I say I don't think my lectures as a whole would be scored this high ...
  
• 79% of students would like other instructors to use the system if they didn't have to buy additional units, but if they had to buy additional units, most students (59%) would not want other instructors to use the system.

The last point is a possibly important one for choosing which system to adopt because I've been told that some manufacturers of in-class response systems charge a per-semester registration fee for students to use the transmitters, even though the students purchase their own transmitters (usually for less than EduCue's system). I've heard this about eInstruction's system as sold through McGraw Hill, but haven't been able to confirm it.

I hope to post a grand summary of how things went this semester, but now is not the time. I've spent all day writing my final exam, grading papers, and soaking in the spa, so I'm wiped out. Additionally, I've got a handful of students questioning their in-class response system grades, so we'll have to see how that gets resolved.

Plumbing Progress

On Wednesday of this week our plumber came by and did a collection of small jobs for us. While we haven't had the best of luck picking contractors so far, our plumber has been great; he's a good guy who appears to do quality work. When our local building inspector checked over the replumbing of our bathrooms he had nothing but compliments, which I take as a good sign.

The two biggest jobs on Wednesday were to install an earthquake shutoff valve on our main gas line (see the picture to the right) and put a second showerhead in the master bath shower. The inspection we had done before buying our house recommended the earthquake valve, which was the first time I'd ever heard of them. The valves are functionally pretty simple; from what I can tell they contain a little ball that rolls off a perch during an earthquake, shutting off the gas. Installing it was relatively cheap: ~$150 for the valve (manufactured by Pacific Seismic Products), ~$90 for labor, and some additional for permit fees. What's surprised me is that almost no one I've talked to around here has ever heard of the things, even though we're in earthquake country. I grew up in California, so I'm not paranoid about earthquakes, but I figured that a few hundred dollars was worth preventing a post-earthquake gas fire. But then again, since nobody else seems to have these valves, our house will probably just burn down after the neighboring houses all catch on fire ...

The other work was relatively minor. Most of our gas lines had ancient shutoff valves that required a wrench to turn, so we replaced these with hand-turnable valves. Our heater also had a rigid gas line running to it from the wall which we had replaced with a flexible line, again for earthquake safety.

Reaching for the sun

After an exhausting day yesterday it was refreshing to wake up this morning and find the first fully opened leaves on our newly planted roses.

Plagiarism

This will be a brief post, as I have far too many things to do right now, but I'm having a quick lunch and wanted to share (aka vent). In my lecture I dedicate a decent amount of time to discussing plagiarism; I have multiple handouts that I provide to the students on the topic (one has examples of plagiarism and another details how to properly cite literature) and I give a 10-20 minute talk on plagiarism to the entire class before any major papers are due. In that talk I outline literature citation requirements, tell the students that I will be scanning their papers for plagiarism, and that they need to e-mail me their papers so I can scan them for plagiarism.

I started this policy in my second semester of teaching, and since that semester have had relatively few problems with plagiarism. I had thought that my materials and discussion of scanning were working as a deterrent, but unfortunately I was wrong. Last night and this morning I ran my students' papers through Eve 2, a plagiarism detection program that I use every semester, and found that seven papers contained significant amounts of plagiarized material (some >80% plagiarized), and many others had possible examples, though I haven't had time to look through them all. For scale, I've scanned about 55 papers so far.

Thus, I've spent a good number of hours last night, and all of my non-class time today, poring over dozens of websites and student papers trying to document the plagiarism. To do this I print out copies of the websites and highlight all the portions that are shared; each paper is typically plagiarized from at least 2 different sites, and I'm very surprised that my highlighter hasn't run out of ink. To make an official plagiarism report at my campus I have to have first confronted the student about the plagiarism, so I've started doing that today as well.

So, to summarize, it's been a very frustrating and disheartening day. I haven't been able to complete any of the work that I had hoped to do today, and I still have hours more work to do to file these reports with the dean. Additionally this has prevented me from returning the graded, non-plagiarized papers to the rest of my class, so nobody knows their grade going into the final. Looking over the papers (which form a stack on my desk now) just infuriates me.

The only thing keeping me sane today is that, from what I can tell, most of my students didn't plagiarize.

Oh well, dinner's over; I need to go and rearrange my lab exam for tonight's lab.

[updated to fix a few spelling errors]

Blogging as recreation

Pharyngula and Marginal Revolution have nice posts about what blogging is like. Being new to this game I can't talk about how blogging works in the long term, but my SO likes to make the point that when people suspicious of new technology look at new leisure activities, which is what blogging is for me, they immediately relate them not to the person's old leisure activities but instead to the work the person could be doing in the time taken up by the new leisure activity. Thus I've gotten comments from family wondering how I manage to spend as much time blogging as I do considering that I'm so busy at work.

I used to play video games regularly, especially Combat Mission: Barbarossa to Berlin last year (a great WWII strategy game if you've got the time), but I haven't played a single video game since I started blogging. My TV watching has declined, as has my leisure reading, but like Pharyngula and Marginal Revolution my science reading and writing has definitely increased. Thus, instead of stealing time from work, blogging has just become my leisure activity of choice; that it ends up helping with my professional life is a pleasant side effect.

As a final note, I just noticed that Blogger's suggested spelling replacement for "blogging" is "flogging"; I wonder if they're trying to tell me something there.

Tangled Bank Post

Mike at 10,000 Birds has posted the May 19th edition of The Tangled Bank. I didn't get an e-mail in to The Tangled Bank on time for the last edition (I was about to frantically send off a late e-mail when I saw the post was up), so this time was sure to send it in well in advance.

Drywall information

We've been having little success in getting good drywall information. A while ago we contacted eight different drywall companies to get quotes for drywalling our bathroom. Only four called us back:

• one told us that they don't do residential work
• one said they'd call back later (which they didn't)
• one said another employee would call us back (which he didn't, but we called the employee directly only to learn he didn't want the job because we were too far away)
• one gave us a tentative quote over the phone but would want to see the room after we've had the windows done

Another problem has been figuring out what textures are available; it's been nearly impossible to find pictures or descriptions of them. My SO found Mike Bell Drywall, which has a good set of pictures of drywall textures as well as lots of other practical information. I have only one regret with Mike Bell Drywall: they're located in Wisconsin and not California. On a side note, Hometime's Drywall Installation How-to Page looks like a good introduction to the topic.

My SO has also found some resources on popcorn ceiling removal, which is another project we're hoping to start in the not-too-distant future. Before we start we'll have to figure out if there's asbestos in the texturing, which is a concern since our house was built in the 1950's. Removing material containing asbestos is particularly hazardous because inhaling asbestos fibers can lead to health problems; however, if asbestos-containing materials are not disturbed they're usually not a threat. So it looks like we'll probably be able to do the removal ourselves if there's no asbestos in it, but if there is asbestos we'll likely have to hire an expert, or just leave it alone since it's been painted over already.

• Ron Hazelton's Popcorn Ceiling Removal Tips is a photo essay detailing how to remove popcorn ceilings.
  
• Air Tech International sells an Asbestos Testing Kit. Note: we haven't checked this company out yet, so please don't take this as an endorsement.
  
• Utah State Department of Environmental Quality's Division of Air Quality has a page detailing Asbestos Removal Procedures for Homeowners
  
• California Indoor Air Quality program's list of Asbestos Information, which includes (at the bottom) a list of labs that test for asbestos. Unfortunately it was last updated in 2000.
  

In-class response system evaluation

The last week of lecturing is finally here, and as always there's far more to do than time to do it in. Since this is the first semester I've used the in-class response system, I'm excited about getting student feedback on it. A few weeks after the students started using the system I did a preliminary survey (results are in the middle of the linked post) which showed that the students seemed to like the system a lot. What I want to find out this week is if that initial "like" has blossomed into a full-blown love affair, or if the romantic glow has faded from their eyes and they're still "just friends".

In my first survey I asked three primary questions, and I'm planning on asking them again this week (I've summarized the answer options in brackets; when options are separated with a "->" an intermediate answer option will be present)

• How much do you like having the in-class response system (PRS system) in this class? [Like them a lot -> Neutral -> Dislike them a lot]
  
  
• If you had a choice, would you prefer this class use or not use the in-class response system (PRS system)? [Greatly prefer with -> Neutral -> Greatly prefer without]
  
  
• Would you like other instructors to use the in-class response system (PRS system)? [Definitely want -> Neutral -> Definitely don't want]

However, there's clearly more I could ask, and more I'd like to find out. My initial thoughts for further questions include:

• Do you feel that the in-class response system helped you understand the topics covered in this class? [Helped a lot, helped a little, it didn't help or hurt, hindered learning a little, hindered learning a lot]
  
  
• Did the in-class response system help you stay involved/interested/awake in lecture? [Definitely helped -> Neutral -> Definitely didn't help]
  
  
• Did the in-class response system influence your attendance in this course? [Was a major factor in my coming to class, was a minor factor, was not a factor]
  
  
• Did you experience any problems using the in-class response system, and if so, how severe were they? [No problems, minor problems that were resolved, minor problems that were not resolved, major problems that were resolved, major problems that were not resolved]
  
  
• How did your participation in this class compare with participation in other similar-sized classes (~150 students)? [A lot more participation -> Same -> A lot less participation]
  
  
• If you had your way, how many in-class response system questions would you like to see in my future lectures? [Many more -> About the same as currently (2-4 per lecture) -> None per lecture]
  
  
• In the last few weeks of the semester I regularly started class with a review question. Did you find this helpful, and should I keep doing it? [Definitely helped, keep doing it -> Neutral, doesn't matter much -> Definitely didn't help, don't keep doing it -> I missed all of them]
  
  
• Overall, how did you like the way I discussed questions after your responses had been tabulated? [Discussed them for too long, discussed a bit longer than I'd like, just right, didn't discuss them quite long enough, didn't discuss them nearly long enough]

I'd also like to open this up and find out if there's anything my esteemed readers would like asked, since at least some of you have expressed interest in using this system in your own classrooms. I plan on asking some questions on Tuesday and some on Thursday of this week (using the system, of course), so feel free to either e-mail me suggestions or leave them in the comments before then.

Noooooooooooooooooo

Pharyngula has gone off the air! Whatever are we to do???

Note: For those who don't know, the outage is a planned one, due to either Pharyngula attending church and Sunday School or an electrical outage. You pick. I was going to do a Pharyngula-themed post in his stead, but the big pile of papers to grade on the dining room table has convinced me otherwise.

[Update at 6:00 pm: It looks like Pharyngula's back up, with two posts already. Aaaaaaaaah.]

Some cheerful breakfast reading

Seymour Hersh has a new article, "The Gray Zone," out in the New Yorker discussing the prisoner abuse in Iraq. Parts of this article read like a Tom Clancy novel, including things like clandestine intelligence officers interrogating people in secret CIA hideouts across the globe. The sad thing is that unlike a Tom Clancy novel, this is real, and very, very wrong.

Hersh's first and second New Yorker articles, "Torture at Abu Ghraib" and "Chain of Command," are also well worth reading.

Design update

As most of you are probably aware, Blogger has introduced a number of new features. Since it's the end of the semester I don't have time to try out the new templates or investigate switching over to their commenting, but I hope to slowly start revising things in the next few weeks.

I have made one change already: each post's permalink now leads to an individual page rather than the archive page. The largest benefit of this is that the search results now link to the individual post pages instead of the archive pages. All old permalinks should still function, but if they don't please let me know.

Guaranteed Transfer Option

The University of California and California State University systems have started "rejecting" candidates that meet their minimum qualifications for admission. The "rejections" are coming as a direct result of the governor's budget for 2004-2005 which stipulates that the UC and CSU systems should reduce their freshman enrollment by 10% (page 3 of the Higher Education budget summary PDF). This is a significant change for the systems, since the Master Plan for Higher Education in California specifies that every student who meets the minimum qualifications for admission should be admitted, and this has been the recent policy of both the UCs and CSUs.

However, the UCs and CSUs are not completely rejecting the students who meet their minimum qualifications. Instead they're sending letters to the "rejected" students stating that if the students attend a community college and take certain courses they will be guaranteed admission to the UC or CSU campus that "rejected" them. The UC system is calling this the Guaranteed Transfer Option (GTO) and the CSU system has a similar program (termed by some the CSU 45/15 transfer program; link is a PDF).

The Governor's proposed budget includes $1.6 million for the UC system to "to provide counseling services to otherwise UC-qualified freshmen who may enroll in a CCC as a result of the proposed 10 percent reduction in new freshmen" (page 6 of the Higher Education budget summary PDF) and $1.9 million to the CSU system for similar counseling. However, no additional funding has been allocated to the California Community College system specifically to handle these students. The community colleges are getting a 3% growth allocation, but as I've written before, since many colleges have shrunk due to recent budget cuts they're ineligible for growth funds in the current year (or at least I'm told that my campus is).

It seems to be implied that the 3% growth funding is intended to more than cover the anticipated CSU and UC student influx. However, the Faculty Association of Community Colleges estimates that 175,000 students were "deprived of a community college education" in 2003-2004 (PDF of the enrollment report); that's 10% of the state community college enrollment of about 1.6 million students. Thus, in theory, we'd need a 10% growth increase just to cover the students we're already not serving, and even more to serve the additional CSU and UC students.

At my campus things are looking especially grim. Unless we were to add more sections of classes, we simply don't have room for thousands more students. Last fall after the first week of classes our math division was 106% enrolled and the science division was approximately 95% enrolled; this spring our classes were similarly fully enrolled.

At a recent meeting I heard estimates that a local UC was diverting ~2,500 students to community colleges, and a local CSU was diverting ~1,500 students. Not all of those students will come to my campus, but a good fraction of them probably will. If 20% of those students come to my campus (number pulled from thin air), and if 15% of those students are biology majors (estimate based on UC admissions), we could have 120 additional students attempting to take introductory biology for majors this fall. Considering that the total enrollment of that course is only 190 currently, that it always fills during the first week of registration, and that we are not offering any additional lab sections in the fall due to lack of a budget, we have no idea where these students will go if they come to our campus.

To add to the mess that all of this is quickly becoming, none of this is official state law yet. The state budget for the next fiscal year hasn't been approved yet, and won't be for some time. Assembly Bill 2833 (amended text of bill; analysis of bill) and Senate Bill 1785 (amended text of bill; analysis of bill) are attempts to codify the UC and CSU transfer option programs into law, but neither bill has gotten out of committees yet. AB 2833 has just been re-referred to the committee on higher education (bill history), and SB 1785 is currently in the senate appropriations committee (bill history). There's some debate regarding whether these bills are required for the universities to start the programs, as evidenced by the UC and CSU systems both implementing the plans already.

It should be an interesting fall.

Note: I'm not sure how permanent the links to the above bill information are. If they fail, try the California State Assembly or the California State Senate search pages.

A response to Inhofe and two ways to help

I've been busy teaching and grading all day, and about the only things I've read online are related to Iraq and Afghanistan, so this will be another non-biology post; sorry.

• Rivka at Respectful of Otters has posted an excellent response to James Inhofe's recent comments.
  
  
• Ted at Crooked Timber has posted a letter from an Army public affairs specialist in Afghanistan requesting that people purchase pens for children. See the post for all the details.
  
  
• If you're interested in helping out in a larger way, a commenter in the Crooked Timber thread posted a link to Operation Iraqi Children.

Pharyngula & Iraq

Pharyngula is currently the top link for the Google search "decapitated American in Iraq". Not the site I'd expect to come up first for that search, but I'm glad to see that Pharyngula is posting on the topic in his usual blunt style. I couldn't agree more with Pharyngula's summary of James Inhofe.

Of course there's many other good posts out there as well; two I've found recently are by Ted at Crooked Timber and Ogged at Unfogged. Ogged couldn't be more right when he says "If ever leaders wanted to lead, this is the time."

[update 11:50pm 5/12/04: Pharyngula's no longer the #1 link for the search, he's now in the 40's.]

Amazing Cakes & Mother's Day

I spent most of today working on two academic dishonesty cases, and get to spend tonight grading and trying to finalize travel arrangements for an upcoming wedding. Thus today's post is just two quick links.

• Mike's Amazing Cakes has some, well, amazing cakes. If you didn't get your mom a Mother's Day cake, maybe you could hurry up and order one.
  
  
• Pharyngula has a great series of posts related to Mother's Day, talking about mother's hips, mother's milk, "grandmother", and Mother Nature.

Back to grading ...

The Animal Kingdom Celebrates Mother's Day

Since Mother's Day as we celebrate it is very human-centric, and focuses largely on buying Hallmark cards, I thought I'd create a list of the style of Mother's Day cards other species might need to buy.

1. Happy Parent's Day, to the one I call mom and dad
For simultaneous hermaphrodites that self-fertilize.

Simultaneous hermaphrodites are organisms that contain mature male and female reproductive organs in a single individual at the same time. These organisms are also called monoecious organisms, in contrast to dioecious organisms where the male and female reproductive organs are found in separate individuals. Some simultaneous hermaphrodites can self-fertilize, meaning that a single individual combines their own sperm and eggs to produce fertilized zygotes that develop into individuals. The offspring in this case will likely not be clones of the parent (though it is theoretically possible for them to be clones) due to the genetic recombination that occurs during production of the sperm and eggs and the subsequent random combination of the gametes. A vertebrate example of this style of reproduction is the fish Rivulus marmoratus. The coccid Icerya purchasi is an insect hermaphrodite that usually self-fertilizes, though some reproductively active haploid males occur in their populations.

2. Happy Mother's Day, to the one some of my siblings call dad
For simultaneous hermaphrodites that don't self-fertilize and sequential hermaphrodites who have turned female after first being male.

Most simultaneous hermaphrodites do not self-fertilize, and thus offspring will be a combination of the sperm from one individual and the eggs from another individual. The belted sandfish Serranus subligarius reproduces in this style, and during copulation the two interacting individuals trade sexual roles. Most barnacles are also simultaneous non-self-fertilizing hermaphrodites. Even though barnacles are sessile they engage in direct copulation; each individual has a very long penis it extends to find other barnacles.

An individual sequential hermaphrodite can be either male or female, but never both at the same time. These organisms are either born male or female, and depending on the environmental conditions around them can turn into the opposite sex. Sequential hermaphrodites that are born male are called protandrous.

Clownfish, of Finding Nemo fame, are a good example of a protandrous hermaphrodite: the largest individual fish in a group is female, the next smallest is the reproductive male, and the rest are typically non-reproductive. When the largest female is removed from the population the male becomes female, and a non-breeder becomes male. Thus, in Nemo's case Marlin (Nemo's father) should have turned into Marla once Coral (Nemo's mother) disappeared.

3. Happy Mother's Day, to the man we call mom
For sequential hermaphrodites who have turned male after first being female.

Sequential hermaphrodites that begin life as a female are called protogynous. Some reef fish, such as the cleaner wrasse Labroides dimidiatus, are protogynous hermaphrodites. Cleaner wrasses live in groups of 10-15 fish, with the largest being male and the rest female. When the male is removed from the group the largest female will transform into a male.

4. Happy Mother's Day, to the only one who made me what I am
For parthenogenetic reproducers.

Parthenogenetic reproduction occurs when an egg (oocyte) develops without any genetic contributions from another individual. Parthenogenesis is highly varied:

• In some species adults females can choose to produce offspring through either parthenogenesis or sexual reproduction, often by either fertilizing or not fertilizing an egg. An example of this is honeybees, which produce female offspring (workers and queens) by fertilizing an egg and males (drones) by not fertilizing eggs.
  
• In other species only certain life stages have parthenogenetic females, while later life stages are biparental, such as in holocyclic species of aphids like Aphis fabae.
  
• Some species are entirely parthenogenetic and never produce males. The desert grassland whiptail Cnemidophorus uniparens exhibits this trait.

Not all offspring produced by parthenogenesis are clones of the parent. In many species meiosis still occurs to produce an egg, meaning that crossing over (and other genetic effects) can still occur, making the offspring likely to be somewhat genetically different from the parent. In some species, however, eggs are produced through mitosis (mitotic parthenogenesis) and thus the offspring are likely to be clones of the parents.

5. Happy Parent's Day, to the only one who made me what I am
For asexually reproducing animals.

Asexually reproducing animals that do not necessarily produce gametes fall into three general categories:

• Gemmulation involves producing a small clump of cells (a gemmule) that has a protective coating. The gemmule will divide and grow into a new organism given the right environmental cues. Freshwater sponges often produce gemmules to overwinter or to survive the drying out of their ponds.
  
• Budding is an unequal division of an organism through mitotic divisions, wherein a small outgrowth eventually matures into an adult. Hydra, freshwater cnidarians, often reproduce in this style; hydra buds are not produced through any action of gametes.
  
• Fragmentation is when a multicellular organism breaks into two or more parts, with each part regenerating the lost portions of itself. Annelids (segmented worms) and echinoderms (e.g. sea stars) can reproduce through fragmentation. Many of these organisms might not buy a Parent's Day card, however, because determining which of the divided individuals is the parent is typically fruitless.
  
• Fission is often added to lists of animal asexual reproduction, but fission involves the reproduction of a single cell into two or more copies of itself. Since there are no single celled animals, animals cannot reproduce through fission; budding or fragmentation are more appropriate terms.

While some of these organisms, such as sponges, never produce males or females, many of these species can reproduce both asexually and sexually. For instance, hydras can be either male or female, and both males and females can make asexually produced buds.

My SO and I had a debate about how to classify the card these combination asexual and sexual organisms should buy, since an asexually produced hydra could be produced by either a male or a female, and thus could theoretically have either a father or a mother. However, since neither male nor female gametes were involved in producing the asexually produced offspring, we concluded that the offspring in question would thus buy a Parent's Day card, not a Mother's Day card.

And, finally,

6. Happy Mother's Day, mom
For biparental, sexually reproducing organisms.

In light of all the variations above, this seems downright boring: one mother, one father, and no changing sexes.

Thanks to Semantic Compositions, whose holiday themed posts inspired this one.

Roses are planted!

The title says it all: we just finished planting our twelve new roses. Yep, the time is 12:45am. I'm sure our neighbors wondered what the heck we were doing out at midnight in our front yard digging holes illuminated by two halogen lights on a tripod. Actually, our next door neighbor stopped by multiple times today, so at least he knew what was going on. Maybe the rest of them just thought we were hiding our weapons of mass destruction.

I hope the roses appreciate the effort ...

Garden work

Sore (sôr) adj. The condition of feeling like Radagast and SO after four hours of cutting sod and tilling soil in their front yard.

We've made great progress on our mission to remove a 7 by 30 foot section of grass from our front yard and replace it with roses and bulbs. We rented a sod cutter and tiller, and started off using the sod cutter to remove the grass. Sod cutters have to be one of the best inventions since, well, gas-powered tillers. In less than an hour we removed all the grass from the area and had it (somewhat) neatly rolled up. The $40 rental charge for the sod cutter was well worth it.

The tilling was not as easy. After spreading out 27 cubic feet of steer manure and 6 cubic feet of sand (the sand alone weighed ~600 pounds) we started the tiller up. Unfortunately the dirt was pure clay (anybody want to make some pots?) and the tiller was just bouncing off the "soil". We dug some trenches to start the tiller in, and after about three hours of very bouncy tilling we declared the area done. Actually, the tiller was the one who decided to call it quits, as it began belching white smoke on our last pass through the area.

We're just about to head off to lunch with an old student of mine, and after that we get to come back and dig planting holes for our 12 new bareroot roses which are soaking in the back yard.

[Updated to properly label my definition of sore as an adjective, not a noun]

Acupuncture and headaches

A while back I posted a link to an article attempting to show medical benefits of acupuncture for headache pain; in the post I left it up to Pharyngula and his links to discuss the study. The study compared patients in two groups: one where patients received the "standard treatment" and another where they received the "standard treatment" plus acupuncture. Pharyngula and others have commented that the study lacked a critical control group and thus was relatively meaningless. Apparently that wasn't good enough for one dedicated reader, so I'll take a stab at it here.

The comment the reader made was

"Ah, but it depends on the meaning of "control group". I've read more than a few pharmaceutical studies where the comparison is between some new drug and the usual "standard of care", rather than between the new drug and a placebo. That seems to be what's going on in this study, although I would have preferred that their non-control group received only acupuncture, rather than acupuncture+medication."

I see three primary differences between pharmaceutical studies and acupuncture studies that relate to this comment. First, pharmaceutical studies are often dealing with life and death conditions wherein the inclusion of a patient group receiving solely a placebo would be unethical if there is a treatment that has been shown to be effective. Second, many pharmaceutical treatments are perceived similarly from the patient's perspective (e.g. "OK, I'm now getting 3 blue pills a day instead of 3 red pills") and thus the possibility for placebo effects are relatively reduced, especially when we compare the difference in pharmaceutical treatments to the difference between poking someone in the head with needles and not poking someone in the head with needles. Third, many pharmaceutical studies can use non-subjective measures to determine the response to their treatments (e.g. white blood cell counts, pulse rate, respiration rate, body temperature, presence of infectious bacteria, etc.) which reduces the potential for confounding placebo effects. In this acupuncture study, however, the two groups of individuals were treated very differently, and the only measures that experimenters gathered were subjective.

A good analogy is for us to ponder the effectiveness of apples and oranges as projectiles. The acupuncture study is designed so that you're running a comparison of throwing an apple and an orange at one person while throwing just an apple at another person, then seeing how the two people react. The apple and orange person is likely to react more strongly, but is that because the orange is perceived as more dangerous, or because they had two projectiles thrown at them? We can't know. The better design would be to throw an apple and an orange at one person, while throwing two apples at another person. Now both people have two projectiles coming at them, and we can conclusively determine if oranges are different from apples. Or, of course, just throwing an apple at one person and an orange at another person would also work (as the commenter wisely states).

The key point is that the people in the groups to compare must be treated as equally as possible, with the treatment in question being the only difference. The primary missing control group in this study, from my perspective, is one wherein people believed that they were getting acupuncture (or some additional treatment), but were not actually receiving any acupuncture. This type of control group would allow us to determine whether the acupuncture itself is causing a physical change in the patient's headaches, or if simply telling a patient that you're treating their headache will make them feel better (a placebo effect). Never having had acupuncture I have no idea how hard it would be to provide sham acupuncture, but there are studies that have used sham acupuncture before, so it is possible.

It is reasonably likely that the study's results were biased by the placebo effect. Even though participants were randomized to a specific treatment (acupuncture vs. no acupuncture), all participants were informed about the study's methods and goals before the study began. Thus patients in the control group knew that they were not getting a treatment, while patients in the acupuncture group knew they were getting a treatment that others weren't; this is far from the ideal double-blind study. Since the study's measures were all subjective, participant knowledge of the experimental design could easily have skewed the results.

To be fair to the authors, I should point out that they address this issue in the discussion. They argue that other studies have shown that acupuncture is significantly different from sham treatments and other placebo effects with regard to pain management, and thus they weren't obligated to look for placebo effects. I e-mailed one of the authors (Dr. Andrew Vickers) to discuss this some, and he made the point that every study can't do everything at once, and that one should take the body of evidence as a whole and not just focus on one study (both good points). He sent me copies of a few papers that do compare acupuncture with placebo treatments for pain management, and I hope to post a summary of those in the coming weeks.

However, there are other problems with this acupuncture study besides the experimental design. In the methods they use one of the more minimalist descriptions of statistics I've seen, and throughout the results they do not include statistical information that should be present: there are no degrees of freedom, no F statistics, no regression coefficients. For comparison, I'm used to reading journals like Ecology, which have very specific statistical requirements.

It also appears that they have misinterpreted their statistical analyses. For instance take this portion of the results

"Table 4 shows data on use of resources. Patients in the acupuncture group made fewer visits to general practitioners and complementary practitioners than those not receiving acupuncture and took fewer days off sick."

and this portion of the discussion relating to those results

"We also found improvements in quality of life, decreases in use of medication and visits to general practitioners, and reductions in days off sick."

Those three sentences are their entire textual description of that data, excluding the table and the abstract. Based on the data in table 4, however, the P values for the three comparisons discussed in the results are all well above 0.05, and thus the differences are not statistically significant and should not be considered real (P=0.1 for visits to the general practitioner, 0.3 for complementary therapist, and 0.2 for days sick). Including false statements like these (implying there is an effect of acupuncture on certain measures when statistically there is none) is the type of data analysis that makes me skeptical about the rest of their study. [note: I could be interpreting their statistics incorrectly - I'd be surprised if a journal let this type of error slip through; if I am please let me know]

I want to make it clear that I'm not saying that acupuncture has no effect; I'm just saying that this study, by itself, doesn't show conclusively whether there is a real effect of acupuncture on headache pain. I also want to point out that this study only looked at the effect of acupuncture on headache pain, and thus has nothing to say about acupuncture's effectiveness (or lack thereof) on any other conditions.

The reference is: Vickers AJ, RW Rees, CE Zollman, R McCarney, CM Smith, N Ellis, P Fisher, and R Van Haselen. 2004. Acupuncture for chronic headache in primary care: large, pragmatic, randomised trial. British Medical Journal. 328: 744.

Future flowers and fall colors

Some Minnesotan has spotted strange red things growing in his yard. Unfortunately, this Californian is currently cursed with a yard that is nearly 100% grass, and thus I have few similarly pretty things poking up at me. Yesterday we started changing that by spraying about a quarter of our front yard with herbicide so we can make a few planting beds, but progress is going to be slow. In the meanwhile, I'll be envious of the evil red creatures Pharyngula gets to look at every morning.

Since my readers should have something pretty to look at, in lieu of California flower pictures here's a picture from a trip to Utah last fall:


This image also serves as a late entry into this week's Photo Friday contest, "natural".

Rotational Illusions

Someone (or some organization; I can't read Japanese) has posted a number of stunning visual illusions. I've recently discovered that I quite like Op art (even trying my hand at it), so these are pretty cool. (Via Lynn S's 23 Questions post)

Semester End and a Human Clock

The end of the semester is quickly approaching here (3 weeks of lecturing left), and so things are starting to heat up. I've already got a huge pile of grading to get through, and it will only get larger as I have an assignment due or test to grade every week from here on out. We've also recently ordered a bunch of plants from Parkseed, so this week we're going to take out a large portion of our front lawn and replace it with roses, bulbs, and other pretty things. And, to add to all of that, we've put in calls to eight drywalling companies to get quotes for our bathroom drywall. The combination of all of these means I'll be busier than normal, and I apologize in advance for any posting breaks and/or unusual snarkiness. For those who care, there was no post last night because your host fell asleep on the couch at 9pm for a "short nap", was moved to bed by the SO around 2am, and then didn't wake up until after 11am, at which time your host had to run off to office hours.

Since time will be tight for me in the next few weeks, an appropriate site to link to is The Human Clock, which is a website that tells the time via pictures users have submitted. The pictures all include the time in some fashion, including everything from numbers written on a piece of cardboard to license plates or jerseys. (Via Jill.txt)

Home again and ecology lab

My SO is now happily here at home after a month back in Philadelphia. The reunion was even sweeter (or, more appropriately, savory) because two authentic cheese steak sandwiches made the flight as well; they were promptly popped in the oven and eaten. The surprises I had in store for my SO's arrival were some fresh bread, cheese, and berries, along with a newly organized garage, cleaned book-room, and some small remodeling progress (scheduling a plumber and ordering some replacement parts). The best surprise was the garage: when my SO left a month ago boxes and appliances were scattered across the floor and there were only a few paths to get around. I organized the whole thing and cleared enough space to almost fit two cars inside. On arriving home last night I pulled into the driveway, opened the garage door, and waited for the reaction; it was fun.

Even though the flight got in relatively late we had to get up early today to help out with another field lab for the ecology class. This time the students were doing transects and sweep netting in coastal sage scrub habitat. The students were complaining about the heat, which was rather funny because besides being sunny with almost no shade it really wasn't that hot (maybe 90F, 50% humidity).

The highlight of the trip for me was hunting down a grasshopper. We could hear but not see a few hoppers in a grassy area near the transect site, so my SO and I went stalking. We could regularly narrow down the hopper's location to only a square foot or two based on the noise, but because there were so many crossing branches in our field of view it took us many minutes to actually see the hopper, and then it usually jumped before we could net it. After many minutes of searching we finally caught the noise-maker: a slant-faced grasshopper. Slant-faced grasshoppers are my favorite type of hopper; their face angles up very neatly (e.g. this one) and thus they blend in nearly perfectly with grass, and look very cool.

Unfortunately I forgot my camera, so there won't be any pictures from the trip. Sorry.