Wednesday, May 26, 2004

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.

Tuesday, May 25, 2004

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."

Monday, May 24, 2004

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.

Sunday, May 23, 2004

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.

Saturday, May 22, 2004

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.

earthquake valve pictureThe 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.

Friday, May 21, 2004

Reaching for the sun

rose leafing out
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.

Thursday, May 20, 2004


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]

Wednesday, May 19, 2004

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.

Tangled Bank Blutton

Tuesday, May 18, 2004

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.

Monday, May 17, 2004

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.

Sunday, May 16, 2004


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.

Saturday, May 15, 2004

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.

Friday, May 14, 2004

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.

Wednesday, May 12, 2004

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.

Tuesday, May 11, 2004

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.]

Monday, May 10, 2004

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.
Back to grading ...

Sunday, May 09, 2004

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.

Saturday, May 08, 2004

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 ...

Friday, May 07, 2004

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]

Thursday, May 06, 2004

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.

Wednesday, May 05, 2004

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:

Fall colors

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

Tuesday, May 04, 2004

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)

Monday, May 03, 2004

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)

Saturday, May 01, 2004

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.