Friday, January 30, 2004

Boxes and bookstores ...

Our house is still completely filled with boxes, but now we've got both of our computers set up so it's at least livable. It's probably a good sign you're a geek when your computer is the last large item you pack (we packed it after the bed, dining room table, and entertainment center) and the first item you set up in your new house (we still don't have our TV plugged in or our bed frame assembled). I'll be spending much of my spare time for the next few weeks unpacking ... whee.

Oh, and to prove what a wild and crazy life we lead, we spent our first Friday night together in CA out shopping for floor lamps at IKEA. We found some good cheap ones ($8 each!) and now can actually see at night in our house :)

Our semester starts next week and so I've spent much of today preparing. I'm using a new response system in lecture this semester (more on this at a later date) that requires the students to buy a little transmitter; they'll use these to answer questions in class and get participation points. In order to get a discount on the transmitter I had the publisher bundle the transmitter and textbook, cutting the cost of the transmitter by >50%, but only after getting confirmation that the bookstore could sell the transmitters separately so students could buy used books (or share books, etc.). Considering that the whole point of the publisher doing the bundle is to encourage new book sales, I was happy that they were willing to sell them separately. I wrote multiple memos to the bookstore explaining the details of this setup, and what did I find upon checking the bookstore yesterday? The nice new book/transmitter bundles were in-stock, but there were no individual transmitters or used books.

I talked with the bookstore ordering manager and he said that they didn't want to stock the transmitters because it would encourage students to not buy the new books from the bookstore. I agree with that reasoning somewhat, but they're forgetting that many students share books (e.g. siblings taking the same course), and that other students get hand-me-down books, but every student must have an individual transmitter. And what's wrong with letting students save money by buying used books online? I finally got him to agree that students could come by and special order the transmitter, but he wouldn't even give me a price. Then, today, I got a call saying that for some reason they can't special order the transmitters. I've given them the publisher's information (and e-mailed the publisher), but haven't heard anything back yet. Hopefully we'll get this figured out ... and at least it should be better than the semester they ran out of dissection kits just before our first dissection lab :)

Back online in CA

We're finally moved! The move took longer than planned, but we're here. We were originally planning on leaving Tuesday, but packing and my SO's work schedule delayed that. We ended up doing the drive on Wednesday after about 4 hours of sleep in our empty house, using down jackets as blankets (the real blankets, mattress, and pillows were all packed). Then, after arriving in CA around midnight, we had to wake up early, unload the truck, and return the truck before the deadline, after which I had to head into work for the rest of the afternoon. Isn't moving fun?

I have gleaned from this experience one good study tip for anyone taking Human A&P: move. Focus on heavy items like washers, fridges, and boxes of textbooks. After about 3 days you'll know the positions of all your muscles by heart; trust me.

On a more personal note, I'm amazed at the wonderful feeling that comes of knowing neither of us has to catch a plane or drive away in a few days. It's, well, odd. But nice. Very nice.

Monday, January 26, 2004

Still packing

My SO is currently at work, and I'm awake and packing. Normally this wouldn't be unusual, but unfortunately we have both been awake since 8am yesterday morning. We pick up our rental truck mid-day today, and have some friends coming by in the afternoon to help us load, so we have to get all our work done and everything packed and ready to go by today. My SO's spent most of the day at work; the sole break was picking me up at the airport (and having dinner afterwards). Fun fun :) Oh, adding to the joy is that all of this work is going unpaid – the grant my SO was working under ran out, so all the time has been on a volunteer basis.

I'm quickly running out of things to pack, so unfortunately my computer will probably be the next to see a box. We'll hopefully arrive in California on Tuesday evening / Wednesday morning, and I'll try to post an update then. Have a great week!

Sunday, January 25, 2004

Heading back to town ...

Today my little vacation is ending; I’m flying away from northern California and into the joys of moving and classes starting anew. The coming few days will be pretty hectic as we’ll be officially closing on our “old” home, moving out to California, and I’ll be beginning prep-work for the semester that starts in a little over a week. Fun fun.

Since I’ve been living in California for the last year and a half, moving shouldn’t be too bad, as about half of our stuff is in California already. Unfortunately, that means that half of our stuff is still NOT in California, so we’ve still got a lot to move. My SO has been frantically wrapping up work, coordinating all the little details relating to the house sale, and doing more packing while I’ve been up here relaxing. And, believe it or not, this trip was largely my SO’s idea! My SO is so wonderful ...

Saturday, January 24, 2004

Unknown unknowns

I spent much of today visiting with family - both my grandparents and my dad/step-mom. I just got the page proofs of my in-press journal article yesterday, and today my dad and I spent a fun hour or two chatting about the study and statistical analyses. Overall it was a good day.

My dad and I also discussed the recent press's handling of Donald Rumsfeld's "unknown unknowns" comment (see for example The Guardian). As my dad so eloquently said, "I don't exactly look for reasons to defend Mr. Rumsfeld from the press ..." but this recent series of jabs seems totally uncalled for. Here's the full Rumsfeld quote:

"Reports that say that something hasn't happened are always interesting to me, because as we know, there are known knowns; there are things we know we know. We also know there are known unknowns; that is to say we know there are some things we do not know. But there are also unknown unknowns - the ones we don't know we don't know." (from The Guardian)

I'm not saying the statement is a paragon of clear speech, however, the term "unknown unknowns" is not nearly as illogical as many reports seem to make it out to be. It's a term that was used in the space programs of the 60's and 70's (and possibly in other places before that, I don't know) to represent variables/items that engineers didn't know to pay attention to. Its abbreviation "unk-unks" is included in at least one list of military jargon, so I'm suspecting it's also used in the military.

Probably the easiest way to think about the term is that we can (as Rumsfeld explains) break our knowledge into three broad classes. First, there are things that are known, and thus we know that we know them; they are known knowns. For instance, we know that the high temperature in San Francisco, CA on Jan 23, 2004 was 53F.

Then there are things that we know exist, but that we don't specifically understand or know their state. These are known unknowns (in other words, variables that we don't know the value of). An astronomical example of this is "dark matter," which we know exists but do not know for certain what it is composed of. Another example is that we know San Francisco will have some high temperature tomorrow, but we don't currently know what that high temperature will be; it's a known unknown. If we wanted to, say, predict how far some insects could fly tomorrow we might want to pay attention to the high temperature tomorrow (our known unknown), and possibly try to model it.

Then, finally, there are elements of the world that we do not know exist. These elements are unknown unknowns. If you're trying to mathematically model something you could consider these as unknown variables; variables we don't even know about. The phrase thus serves as a useful tool to remind us that there are many things that are completely unknown (and thus we should attempt to search them out and/or plan for them).

A biological example of an unknown unknown I can think of is to go back in time, say, a hundred years and ask someone to model how far an insect could fly tomorrow in San Francisco. That someone would clearly know to consider the high temperature tomorrow (our known unknown), but they wouldn't know to ask what type of myosin/actin fibers are in the insect's muscles, since proteins hadn't even been discovered yet. In other words, the muscle fiber type was, a hundred years ago, an unknown unknown; nobody even knew to consider it when thinking about insect flight.

Another good example of an unknown unknown my dad thought of was the cellular damage caused by radiation. When early researchers were studying radioactive materials they knew certain things about the materials they were dealing with (their color, size, shape, etc), and they knew that there were certain things they didn't understand (e.g. what was being lost from an atom when it decayed). However, nobody knew that it was even possible that radiation would damage cellular components and cause disease; that was an unknown unknown (which lead to many untimely deaths).

From a teaching perspective I think the phrase may also be quite useful, as it conveniently describes the variables students don't know to pay attention to in their experiments because their world view doesn't include them (at least in relation to that specific experiment).

Friday, January 23, 2004

Kissing slugs and eating insects

It was my uncle-in-law's 40th birthday today, and during dinner I got to talk with my cousin about her experiences at a 5th grade camp she just got back from. She got to do lots of neat stuff – visit some tidepools, kiss a banana slug, and go on a night hike (complete with an area where the students walked alone in the dark). The hike reminded me of a Card Captor Sakura episode where the kids have to walk alone through a cave and one of the teachers jumps out of the shadows and scares Sakura. Unfortunately they didn’t do anything nearly as cool at my cousin's camp (and the night path was lined with counselors hiding out of view ... lame).

What I found most interesting, though, was my relatives' disgust upon hearing that my cousin kissed a banana slug. This got them discussing various other "disgusting" foods people sometimes eat on reality shows like maggots, earthworms, and various organs. Even though my cousin seemed to not have any cares about kissing a banana slug, I can't help but wonder how conditioned to hate invertebrates she'll become after enough of this kind of talk.

This then got me thinking about a good paper I read a few years ago reporting on the widespread consumption of insects in many countries/cultures. Insects are available in large numbers, they make excellent protein sources, and they've been used as food sources (probably) throughout all of history. It seems likely that western cultures are the oddballs for disliking insects. However, as cultures become more and more influenced by western values, they absorb our hatred/disgust of insect consumption, stop eating insects, and instead try to buy much more expensive cow, pig, or chicken meat. Since the meat is now too costly, people don't eat enough protein and thus become malnourished. This, to me, is a sad example of how one culture's irrational phobias can lead to significant harm when those fears get transferred to another culture

The article also had a few other neat tidbits. When Mexican agriculture ran into a grasshopper/locust problem a while back, one of the options they considered was to hire a number of workers to pick off the grasshoppers and use them as food. Unfortunately pesticides won out. Additionally, winged termites are apparently delicious. Many people seem to consider them better than the best steaks, and thus I've desperately wanted to try them since reading the article (but haven't found any).

DeFoliart, G. R. 1999. Insects as Food: Why the Western Attitude Is Important. Annual Review of Entomology 44: 21-50.

Thursday, January 22, 2004

Grandparents, chickens, and a modem

I’ve now switched locations to my Dad’s house, and unfortunately the only connection to the net that I now have is a dial up modem and a computer that I strongly suspect is powered by coal (or maybe koala bears). I don’t know how I survived life with a dial up modem. Heck, the software on this machine is so dated I can’t download file attachments at one of my mail accounts.

I did get to visit with my grandparents today – they’re neat people. I’d heard from my folks that they weren’t doing too well, so was worried about how they’d be when I visited. However, they were as perky as the last time I saw them when they were well (the last time I saw them my grandfather was coming out of triple bypass surgery), and my step-mom said that she hadn’t seen them this perky and chatty for a long, long time. My grandfather used to work for NASA/AMES as an aeronautical engineer, and we chatted for a while about some of his old work. Both he and my grandmother have some great stories, so it was a fun afternoon.

My grandfather knows that I’m a biologist, so at one point we were comparing the design of bird and plane wings. Interestingly (and also intuitively) he mentioned that a lot of early engineering work on plane wings was based on the analogous bird structures. Birds, however, played a much different role in some of his design work in wind tunnels. To test the ability of jet engines to withstand the impact of foreign objects they would throw frozen chickens into the running engines; not exactly the kind of real-world contributions ornithologists like to brag about :)

Wednesday, January 21, 2004

A good day and a good quiz ...

I spent today largely in Berkeley enjoying the wonderfully liberal atmosphere. It's hard to say whether the highlight of the day was the hour long massage or the hour spent in a wonderful little tea shop near the Berkeley campus sipping a fragrant cup of Lapsang Souchang tea and having some great conversation.

In my brief web browsing today I found a great quiz entitled 'Should I get a biology PhD?'. If you're wondering whether you're a good organismal biologist, take this quiz! Unfortunately, answering honestly only gets me to med school ... though I do find the "correct" answers to be quite accurate (and hilarious).

Tuesday, January 20, 2004

A House Divided ...

One of my first comments on this blog was from another biologist (Pharyngula) on how happy he was to have a year's worth of separation from his wife behind him. Since I'm traveling this week apart from my SO yet again, and Pharyngula has just discussed some of the challenges of academic life while having a family, I thought I'd describe my separation for the past year and a half.

It all started about 2.5 years ago, when my SO was looking for a new job. My SO was applying for research tech jobs in-state, and for one job they asked, "So, are you thinking of moving anytime soon? We'll need a long term commitment." At the time I was an adjunct looking for jobs on both coasts, and I felt I had about as much employability as a caterpillar. In the end my SO took the job and the long term commitment.

Less than 9 months after the 2-3 year commitment was given, a community college in California decided that caterpillars make good professors, and hired me. Since the position was too good to pass up (for many reasons, including the minor details that we'd be living near old friends, I'd get to develop a new course, and my salary would increase more than threefold) we ended up doing what I imagine many academic couples have done: we split the household.

We don't have kids, so that probably made it easier. We were close enough that flights could be gotten relatively cheaply, and driving wasn't out of the question. We used IMs, voice-over-IP, e-mail, and (gasp) the phone. We visited every other weekend when we could. In the past semester (while we were selling our house) I spent at least 10 of the 16 weekends during the semester out of town, most of those visiting my SO.

We spent all of our long vacations together. In some ways the separation was good, because it let each of us focus on our very time intensive jobs, and it also reinforced for us (or at least me) just how precious we both were to each other. But it was also stressful, and I'd be eternally happy if I never again saw that same, long stretch of highway I got so used to driving. It also hurt both of our job performances -- whenever we were together the last thing we wanted to do was work, even if it was the entire month of January that we were spending together. We both installed IM's at work, and chatted for long periods of time every day. And heck, there's no way I could leave town 3 days a week for 10 weeks during a semester and do as good a job as I'd like to.

However, what it also taught me is that we were far from alone in our separation. I know of at least two other faculty members who live in split academic households at my current school, and the scary thing is that both of them have been doing it for years. And with at least some folks hoping for a backlash against spousal hiring (for very good reasons, I might add), I wonder if the trend will become more common. At least my SO and I knew that it was going to be temporary -- initially we thought that within 6 months it'd be over, though that 6 months extended to a year, and then a year and a half, but we'll ignore that. In any case, we knew it was temporary and that we were moving to an area where finding a job for my SO shouldn't be impossible. I guess I can understand why couples would do a split household permanently (life happens despite our best intentions, and I'd far rather live in a split household with my SO than without my SO), but the stress and frustration are something that nobody needs.

I'm not sure that this post really has an academic point, but one question that I'm coming to is this: how can academia (or society) help those individuals who live in a split household? My campus showed incredible understanding -- my teaching schedule was compressed to fit into 3 or 4 days so I could travel easily, I wasn't given much committee work, I was able to do work remotely, and my students put up with delayed e-mails and slowly graded papers, but I can't imagine that happens everywhere. And for those people who have kids, I don't even want to think about the stress that they add to the picture.

I guess a second point of this post mirror's Pharyngula's: if you're considering going into academia, be prepared for hard relationship decisions and non-ideal living conditions. I know of many couples who've never had to live apart, yet I know of some who've lived apart for more than a decade.

But for now, for us, our separation is nearly at an end. After my trip ends we'll load up our moving van and head out to California, where we'll both be living under the same roof. And, for the first time in a very long time, we don't know when that joint tenancy will end.

Monday, January 19, 2004

Internship offered!

A few hours after the phone interview this afternoon my mom got another call from the congregation and was offered the internship! YAY! This is very good news for her since the internship is the next required step of her program (and she'd already gotten a few no's from other places). Go mom!

Parent interviews

I'm currently visiting my mom, who is, of all things, on the phone right now interviewing for an internship with a UU ministry in the New England area.

Let me go back in time for a bit and explain. For most of my life my mom was a business manager at various companies, eventually becoming a vice president at a startup. She was about as outwardly religious as the average grasshopper (though maybe they're quite religious, I don’t know), and I can probably count on both hands the number of times I was in a church while growing up. Imagine my surprise, then, when one day in graduate school I received an e-mail from her saying that she was going to be quitting her job and would be attending a seminary (OK, it didn’t happen quite that suddenly, but I can dramatize, can't I?). So, just as I was leaving graduate school and starting my adjunct teaching, my mother was quitting her job and going back to school. It has made for many interesting discussions, and has overall been rather inspirational (definitely drives home the message "do what you believe in and enjoy").

So, now that a few years have passed and my mom is nearly done with her coursework, she's applying for internships at various congregations across the country. This is, to put it mildly, odd. For instance, my mom and I have spent a decent amount of the past day preparing for her interview. We've walked through possible questions, discussed the congregation she's interviewing with, talked about how she can explain her theology, and just generally dealt with her stress. We spent the last hour trying to find ways to distract her from the impending phone call (which discussions of state politics and education funding did wonderfully). I never thought I'd be the one helping my mom deal with pre-interview stress ... that's just not something "kids" are supposed to do :)

Sunday, January 18, 2004

Plane experiences

I'm now in northern California - the flight was largely uneventful except for two things. First, after the plane reached cruising altitude the stewardesses came around with the drink cart (no, that wasn't one of the two big events). I put down my book (The Two Towers - finally decided to re-read the LoTR) and folded down my tray table. Plastered all over my little tray table was a full color ad for a car! What the heck? Did I really pay more than a hundred dollars for the privilege of eating my two bags of salted peanuts while staring at a car ad? What's next, ads on the emergency exit door handles? "Sponsor" messages during the safety video? In any case, it seemed vaguely wrong. On second thought, though, maybe the car ad paid for the extra bag of peanuts ... that did seem like quite a luxury.

On a lighter note, after we pulled up to the gate and the first class folks started getting off the plane, a stewardess came on the intercom and said in a serious voice, "Passengers at the back of the plane: we will be deplaning." Well, I guess that's better than not being allowed to get off the plane, but did we really need to be told that? And what about those of us in the middle of the plane ... were we not allowed to leave? The statement was never clarified, but I suspect she meant to say "we will be deplaning from the rear of the aircraft as well" since they had stairs at that exit, but it was pretty funny as it was.

Heading out of town

I'm off to visit my parents in northern California today, and will be with them for the next week. I should have net access while I'm up there, so hopefully I'll get some posts in while I'm there. Unfortunately my SO isn't coming with me, as she needs to finish her work here before we move :(

Have I mentioned how much I love having a work schedule that gives me multiple weeks off in the winter so I have enough time to take vacations like this?

Saturday, January 17, 2004

Water heater draining

cups with sedimentA few days ago I set out to drain our water heater. Why, you ask? Well, for a while now it had been making popping noises whenever it turned on, and we finally figured out that those noises meant that there was probably sediment buildup in the tank. To take care of sediment buildup we learned that one needs to drain the tank.

I read the instructions on how to drain the tank (which included the statement "the water heater should be drained every 6 months" ... is 4.5 years really significantly different from 6 months?) and it all seemed simple enough. Removing all the jargon the instructions boiled down to one line: "open the spigot at the bottom of the tank, dummy."

So, I opened the spigot. And waited. After a few minutes with a grand total of about 2 drops coming out, I realized that something was wrong. Long story short, it turns out that the sediment (mostly salts) in the bottom of the tank had plugged up the spigot, so I got to spend the next half an hour threading a plastic tie through the spigot to allow the water to slowly drain out.

I collected the first 6 cups of water that I got out of the water heater, and took the picture above after the sediment had settled to the bottom. There were fully 2 cups of sediment in the first 6 cups of fluid.

sediment on the groundOnce the flow got going (I ended up turning on the cold water inlet to the water heater to help force the sediment out) I set up a hose and let the water drain in the gutter, which quickly looked like someone had scattered sea salt across it. All that white stuff in the picture to the left is salt that was once in our water heater. That's a quarter for scale, and that's probably less than one fourth the area the salt was spread out over.

Moral of the story: if you haven't drained your water heater in 4.5 years, it may well be time to do so :)

Friday, January 16, 2004

Two good articles

Now that I know I'll be heading out of town for most of next week, I need to start focusing on packing boxes for my upcoming move. Of course, instead of packing boxes or working on syllabi I've been reading blogs. So, here are two good articles I've found that should make a fine morning's read:

Parasitic wasps "mating" with flowers: A great article by Carl Zimmer about how some orchids fool male parasitic wasps into attempting to mate with them. Absolutely fascinating biology! (of course I say that about every parasite Zimmer brings up, but we'll ignore that)

Evolution of the ASPM gene: Post by Pharyngula looking at evidence that the human primate lineage has had strong selection for the ASPM gene, a gene that may be the cause of our larger brains.

Thursday, January 15, 2004

Robot scientist

Researchers have created a robot scientist that comes complete with the ability to create and test hypotheses relating to yeast genetics (see Nature's highlights here). Now, if they could just make a robot-teacher and a robot-house-remodeler I could finally devote all my time to what's really important in life: blogging.

Ovulation mystery resolved: the data never existed

Two days ago I discussed an article showing that women have multiple waves of follicular development during the ovarian cycle. Yesterday I posted the observation that multiple news sources had cited the same study as showing that multiple ovulations occurred during a single cycle, even though the paper didn't seem to include any multiple ovulation data.

I e-mailed one of the co-authors of the study (Angela Baerwald) to inquire about the discrepancy, and she kindly (and promptly!) replied that there are no multiple ovulation data; all of the earlier waves of follicle development observed were anovulatory. Here's a portion of her response:
The primary finding of our study was that women exhibit waves of follicular development during the menstrual cycle. Only the final wave of the cycle was ovulatory. All preceding waves were anovulatory. Unfortunately, there were a few reporters that could not differentiate between follicular development and ovulation. They took it upon themselves to state that women ovulated more than once a month which was not what we found. As one reporter often feeds off of another, there were a significant number of media reports that focused on multiple ovulations. We sincerely apologize for the confusion.
She also included another paper that provides more details about the multiple follicular waves – it's a great read if you're interested in this phenomenon (see the abstract or a PDF of the manuscript if you want to find out more). Here's a little teaser: it looks like the waves of follicular development occur throughout the entire ovarian cycle and do not just take place during the follicular phase.

So this now looks to be a great example of the media misinterpreting, and misreporting, research results. I'll probably use this in my classes as an example of why reading the primary literature is a very good thing, and just how professional misreporting such as this can sound (all the misreported articles I've found include quantitative descriptions of the non-existent data). Here's an annotated list of the most relevant web sources I've found so far:
Official sources on the paper:
  • Journal's abstract: Very concise and well written; clearly shows the lack of multiple ovulations.
  • Journal's summary of the research: Scroll down to find this paper; this is a good summary that lacks any mention of multiple ovulations.
  • Press release: This is by the Canadian Institute of Health Research, and it's relatively clear that there were not multiple ovulations. However, it does say that for many women there may be an egg ready to ovulate at multiple times during the cycle.
  • Good articles (no mention of multiple ovulations):
  • WebMD: An excellent article that clearly differentiates between ovulation and follicle development, and also extrapolates about why this study shows the rhythm method might not work well.
  • Women's Health Matters: Their article is (entirely?) based on the press release, and as such includes no mention of multiple ovulations.
  • Articles including multiple ovulations:
  • The New Scientist: First line of the article is "Women may ovulate more than once a month ..." and it goes on to say that "ten per cent of the women studied released two eggs in the same month."
  • AZCentral (from the LA Times): Article starts by discussing the belief that women ovulate once a month, and then says that this new study counters that belief, including the statement that "Most of the 63 women studied released an egg just once a month but, in six cases, eggs were released twice." The same article is found at the Sydney Morning Herald.
  • MSNBC: Article starts with "No wonder the rhythm method does not work so well for birth control — scientists in Canada said Tuesday they had found women sometimes ovulate several times a single month." Further along it says, "Thirteen of the women ovulated multiple times, in various different ways."
  • Health24: An article that tries to delve a bit more into the implications of multiple ovulations. It starts off with the first sentence, "...women sometimes ovulate more than once a month" and then later includes that "... only 50 of the 63 women really had normal ovarian cycles. The other thirteen ovulated many times in one month and in different ways." [note: I'm now getting an error that this site may be unavailable for international (non-African) users]
  • The paper referenced above is: Baerwald, A. R., G. P. Adams, and R. A. Pierson. 2003. A new model for ovarian follicular development during the human menstrual cycle. Fertility and Sterility 80:1, pp. 116-122.

    The paper detailing the waves of follicular development is: Baerwald, A. R., G. P. Adams, and R. A. Pierson. 2003. Characterization of Ovarian Follicular Wave Dynamics in Women. Biology of Reproduction 69:3, pp. 1023–1031.

    A new linguistic blog

    A good friend of mine has just started a new blog over at Semantic Compositions. He's a computational linguist, writes extremely well, and he's got some great (and understandable) posts about linguistics up already. Heck, he's already used the name of another biology blog (Pharyngula) as the basis for an article discussing "Cranberry Morphemes." Go take a look!

    Mars rover is off and running!

    NASA's Mars rover Spirit has left its landing pad and is now on the surface of Mars! Spaceflight Now has a good article describing the procedure; they also have a great mission status center which has regular updates and pictures from the mission (NASA's site has even more pictures). If you're wondering what the rover's going to do in the next few weeks there's also a good article on the exploration plan.

    Wednesday, January 14, 2004

    Multiple ovulations?

    Yesterday I described a study showing that women have more than one wave of follicular development per reproductive cycle (see the post here). Interestingly, some media reports have included that the same study showed conclusively that women can ovulate more than once per ovarian cycle. The New Scientist and AZCentral both state that 6 of 63 women ovulated more than once (thanks to Amity Wilczek at Nature is Profligate for finding these, and for discussion that helped with this post). MSNBC states that 13 of 63 women ovulated more than once "in various different ways."

    What's odd about these statements of multiple ovulations is that I can't find any reference to these data anywhere in the paper. The abstract includes data on only 50 women, the journal's summary of the research makes no mention of multiple ovulations, and even the press release I found doesn't mention multiple ovulations. Amity Wilczek found the full paper and says that it doesn't mention anything about multiple ovulations either (other than saying that the 50 women only ovulated once).

    The paper does include that there were 63 women in the study, with 13 removed for various reasons. The reason those 13 women were removed were "1 woman had an interovulatory interval less than two standard deviations from the mean, 4 women exhibited luteal phases shorter than two standard deviations from the mean, 1 woman had an ovarian dermoid cyst, and 7 women developed an anovulatory follicular cyst, hemorrhagic anovulatory follicle, or luteinized unruptured follicle during the study" (quote from Amity Wilczek at Nature is Profligate).

    So, I'm left wondering where these data on multiple ovulations are coming from. Are they in a separate paper that the articles aren't citing? Are they included somewhere in the paper and I'm just missing them? Is it a misinterpretation of the paper? Or do these data just not exist? A mystery indeed ...

    Tuesday, January 13, 2004

    Blood donating ...

    I went and donated blood today, and am embarrassed to say it was my first visit in a year and a half. They'd redesigned the donation center since my past visit and after I asked, "Oh, when'd you do that?" they kindly answered, "a year ago." Heh. Heh. Here's hoping I don't miss any more remodels.

    If you're interested in donating (in the US), check out the Red Cross or United Blood Services (or whoever else is in your area). In looking through the Red Cross's stats, apparently 1/3 of male donors aged 25-44 donate for the first time because someone encouraged them. Therefore if you're male, 25-44, and haven't donated blood yet, I'm officially encouraging you.

    Curious about eligibility? See the Red Cross's eligibility guidelines. Of note is their section on Marijuana: "Acceptable as long as you are not under the influence of marijuana at the time of donation."

    Human follicular development

    I teach the human ovarian cycle in my class as an elegant example of what happens when you have multiple hormones with complex, yet understandable, interactions. It's a neat, fairly well understood system, so you can imagine my interest when I found an older entry on Nature Is Profligate citing a recent study showing that the cycle doesn't work quite as I understood.

    Women's eggs are stored as undeveloped follicles that mature during the ovarian cycle. Follicular development is typically described as a process wherein one follicle leisurely matures, and once it reaches maturation, ovulation occurs (with a number of hormones playing a role). More detailed textbook descriptions often include that multiple follicles are stimulated to develop at the beginning of the cycle, but that after a week or so all but one of the follicles typically regress. In both cases, however, the process is usually presented as a steady progression from an undeveloped follicle to a mature follicle that is ready to ovulate.

    However, it appears that women almost always have multiple waves of follicular development. A recent study (see both the paper's abstract and the journal's summary of the study) used ultrasonography on 50 healthy, regularly menstruating women to examine their follicular development (sidenote: that's some detailed ultrasound!). They found that 68% of the women had two waves of follicular development, and the rest of the women (32%) had three waves of follicular development. Based on their data it looks like no women had a single wave of follicular development. It appears that most women ovulated only once, meaning that the follicles in the first wave began development and then regressed, allowing another set of follicles to develop afterwards.

    So how could we explain these multiple waves of development using classical hormone models? A rise in follicle stimulating hormone (FSH) causes follicles to start developing, and the developing follicles produce estrogen which then reduces the levels of FSH by negative feedback (until just before ovulation, but we'll ignore that). On first glance it seems that we can understand how a 2nd wave would start after a follicle regresses: the regressed follicle stops producing estrogen, which releases inhibition of FSH, leading to a subsequent rise in FSH and thus stimulating another follicle to develop. (Note: I'm extrapolating here, and I've removed gonadotropin releasing hormone and luteinizing hormone from this discussion to simplify things)

    But my question is this: what causes the waves of follicles to regress in the first place? Would that be under hormonal control, cellular control, or some combination? Any thoughts? Any other neat work on this topic?

    Have I just been the victim of oversimplified textbook descriptions all along?

    The paper referenced above is: Baerwald, A. R., G. P. Adams, and R. A. Pierson. 2003. A new model for ovarian follicular development during the human menstrual cycle. Fertility and Sterility 80:1 pp. 116-122.

    Monday, January 12, 2004

    Knowledge checks: an apparently successful assignment

    Unlike most folks my semester doesn't start for another few weeks, so this week I'm doing general planning for next semester and analyzing student feedback from last semester. I just got finished looking at data from last semester's Zoology lecture, and one assignment, weekly knowledge checks, stood out from the rest. Here's why:
    97.8% of students said the knowledge checks either "helped a little" or "definitely helped" them understand the course material, while only 2.2% said that the assignment was "no help at all" (63% answered "definitely helped"; 34.8% answered "helped a little").

    89.1% of students "would prefer the course with knowledge checks," while 8.7% "would prefer the course without knowledge checks" (2.2% were "not sure / intermediate").

    (data based on voluntary in-class anonymous surveys distributed at the end of the semester, n=47)

    Considering that the knowledge checks were an assignment that took at least half an hour outside of class each week to complete (and many students spent much more time than that), I consider that to be pretty good feedback.

    Knowledge checks are essentially weekly review quizzes that I administer online using course management software (WebCT, though others like Blackboard would work). I post each knowledge check after my last lecture of the week, and each student must complete that knowledge check by the start of next week's lecture (they have ~5 days to complete them including a weekend). As a concession to possible technical or other problems I drop their lowest two grades. The knowledge checks end up being worth 120 points out of ~500 points possible for the course. The questions are based primarily on my lecture, and focus on comprehension of terminology and basic concepts.

    What differentiates knowledge checks from typical weekly quizzes is that I allow each student to take each knowledge check up to 5 times, and only record their highest score. After each attempt the student can immediately see how many points they got, both for the entire knowledge check and for each question (the latter is essentially a "right" or "wrong" indicator, though for multi-part questions this gives an idea of what proportion of answers they got correct). The knowledge checks are open book and open note, and the students can spend as much (or as little) time as they want on them.

    My main goal with the knowledge checks is to encourage students to keep up with course content; I don't think of them as a tool to evaluate individual student comprehension (I feel papers and tests better fill that role). The majority of students get 90-100% correct on the knowledge checks, and almost all students retake each knowledge check multiple times to achieve as high a score as they can. I know that many students view the knowledge checks as "free points," though I suspect that this belief motivates students to work harder on the assignment (e.g. "I want to make sure I get a 10!") and thus helps the assignment achieve its pedagogical goal.

    I quite enjoy having knowledge checks in the course; they motivate student questions (and office hour visits), help keep the students up-to-date with the material, and give me weekly feedback about how well students have grasped various topics. In fact, I typically start each week's lecture by discussing any recent knowledge check questions that students had significant trouble with.

    I'm curious what suggestions/comments folks have on this assignment, as well as what other types of coursework people use to keep their students up to date on lecture material.

    Two good topics

    Pharyngula (another organismal biologist, yay!) has some excellent recent posts:

    1) Missouri has introduced an Intelligent Design / Creationism bill. Pharyngula sums it up best by calling it "another stupid bill." See more information in Pharyngula's three excellent posts:the first post summarizes the bill and includes contact information for the bill's legislative sponsor, the second post discusses the bill more, and the third post examines the organization that is thought to be sponsoring the bill.

    2) Pharyngula also has an excellent two-post review of Carl Zimmer's new book Soul Made Flesh (see the two posts here: first post, second post). I absolutely loved Zimmer's Parasite Rex, so now I'm looking forward to picking up a copy of Soul Made Flesh.


    A good friend of mine who studies computational linguistics was just officially awarded a patent, co-authored with a number of other folks. I just wanted to take a moment and send him some congratulations - he's worked long and hard on this!

    Sunday, January 11, 2004

    Valley of the Kings

    I just saw a neat program on the Valley of the Kings last night, and today found an excellent resource on the site. The program I saw focused on the excavation of the tomb of the sons of King Ramses II, known as KV 5. The tomb was found in modern times in 1825, but the entrance was covered by excavation materials from another tomb and only rediscovered in 1987. Before 1990 they parked tour busses over portions of the tomb, damaging a decent amount of it. Good job, people.

    KV 5 is an incredible tomb - it isn't fully excavated, but it's at least 443 meters long, and covers more than 1200 square meters. It's one of the largest tombs in all of Egypt, and I think most of it was excavated out of solid rock. Wow. The linked site has an incredible amount of information on the tomb itself (if you have flash, try out the "Launch this site in the KV atlas" feature).

    The Theban Mapping Project has a ton of wonderful information on the Valley of the Kings, containing detailed descriptions, maps, and photographs of all the various sites. In reading this over I'm amazed both at how relatively little we know about these tombs (many are still partially excavated or completely filled with debris), and also how badly the tombs have been treated. For instance, KV 3 was converted for use as a coptic chapel, KV 4 was both used as a stable and as Howard Carter's dining room, KV 9 contains Greek and Roman graffiti, and KV 17 's decorations were largely destroyed by early archaeologists.

    Saturday, January 10, 2004

    Farmed vs. Wild Salmon

    Recent reports indicate that farmed salmon contains higher levels of pollutants than wild salmon. The cause of these increased levels is likely the salmon's feed, which is an oil-rich food containing ground up fish. This seems like a good example of how relatively low levels of pollutants in the environment can become concentrated in animals that are higher up in the food chain (though, in this case, the process is aided by humans).

    Another related example of this phenomenon occurs during algal blooms, wherein toxins produced by algae are concentrated in algae-consuming animals (e.g. mussels, anchovies, krill). Thus, during algal blooms, animals that eat those algae-consuming animals (e.g. humans, sea lions, whales) may receive potentially lethal doses of the toxins (see this UCSC press release for an example of this in Monterey Bay).

    It's unclear what levels of the pollutants found in the farmed salmon are safe for humans. The LA Times (article free with registration) reports, "None of the high levels exceed standards set in 1984 by the Food and Drug Administration for commercially sold fish. But they are higher than the guidelines set by the Environmental Protection Agency in 1999 for recreationally caught fish, which are 40 times more restrictive."

    I'm quite impressed by the variety of locations the study sampled fish from (multiple locations in both the US and Europe it seems), as well as the number of fish they used (apparently 700, at least some of them bought from markets), and the number of "contaminants" they sampled for (around 50). It'll be nice when I can get my hands on the actual paper.

    Toxins aren't the only reason to examine farmed salmon, though, as the industry doesn't seem to have a great environmental record either. A good article from Mother Jones (a very left-wing source) brings up some concerns regarding the environmental impact of modern salmon farming, including (among others) their use of antibiotics/antiparasitics, introduction of non-native salmon species, and production of huge amounts of waste.

    I've chosen to avoid farmed salmon for a while now (largely due to the environmental reasons listed above), though even with the toxins and environmental problems I suspect eating farmed salmon is probably healthier than eating a bacon cheeseburger.


    I woke up early this morning, and watched a full episode of CHiPs. I absolutely loved CHiPs as a kid, and watching it this morning reminded me why this is one of the many shows that fit into my "I can't believe I actually watched this" category. The plotting is terrible (at one point the officers are chasing a hijacked bus, but then drive a car onto 2 wheels and completely forget about the chase, letting the hijackers get away), the extras were completely unbelievable (bus passengers who are being hijacked look like they're being shown a movie on the minutiae of paint drying), there was so much superfluous "action" that the actual plot took less than half the episode, and the dialogue was just bad.

    However, after doing some searching online I discovered a few redeeming factors for CHiPs. First, Michael Dorn (of Worf fame) was on the show as a regular for a few years, though he's hardly recognizable beneath the 70's moustache. And second, who couldn't love a show with such stunning episode titles as, "Drive, Lady, Drive" (parts I and II), "Go-Cart Terror", and "Valley Go Home!".

    And heck, even though it was a terrible show, I must admit that I had a blast watching it :)

    Friday, January 09, 2004

    Termite companies ...

    I just got done paying our termite treatment company $125 for a warranty extension that was necessitated mostly by their own delays ... grr. Here's the story:

    When we bought our "old" house it was treated for termites and came with a termite warranty that ended in early December 2003. We'd found termites in the house once before, and the company treated them relatively promptly (it took 2 months, but it got done).

    Then, in October of this past year we noticed more termite trails on our walls. We called the termite company, but they didn't return our call. We called again. No return call. Finally on the third try someone called us back and scheduled an appointment for late November (the soonest they could schedule us). We let them know that our house was now on the market, and that we might be out of town on the treatment date, so they should contact our realtor if they had any problems.

    We were indeed away on the treatment date, and upon hearing nothing we assumed that all had gone through as planned. Bad us. December arrived, our termite warranty expired, we got an offer on the house, and we learned from our realtor that no termite work had been done.

    True, we weren't home at the time of the appointment, but the least they could have done was left a message saying they'd missed us. Heck, our realtor's phone number is printed in 2" high numbers on a big white sign in our front yard. How hard would it have been to just call that number when they found nobody home?

    The termite company said that since our warranty had expired we'd now have to pay for all the termite treatment work (in addition to any warranty extensions we wanted). We were, to put it mildly, not happy. After some calls by our realtor we ended up "only" having to pay for the warranty extension (which we were considering doing anyway), and not for the treatment work, but it still seems slimy.

    Isn't selling a house fun?

    Textbook costs

    Pharyngula recently lamented discussed the high cost of textbooks, and I agree with his comments. Textbooks are quite expensive, and many students have trouble paying for them. Courses cost $18 a unit where I teach, so students regularly spend much more on their books than they do on registration fees for the course.

    However, I’ve recently had the opportunity to see just how much work goes into making a textbook by participating in a focus group for an upcoming 2nd edition of a biology text (Freeman). In some respects I’m now amazed at how relatively cheap modern textbooks are.

    Modern introductory biology textbooks are usually at least 500 pages long, printed in full color, and contain professionally reviewed material that is usually no more than 2-3 years out of date at the time of printing. All the biology books I’ve recently looked at include comprehensive student CDs that contain supplemental content for every chapter in the book (usually including animations), as well as a book website with review questions and more content. In addition to the textbook and student materials, the publishers of books I’ve looked at generally provide instructors with a tremendous amount of supplemental material, including pre-printed transparencies, printed instructor’s guides (usually including a test bank and chapter outlines, at the least), instructor CDs full of content (test questions, discussion questions, figures from the book, animations, video clips, PowerPoint presentations, etc), course management software packs (e.g. content for WebCT, Blackboard, etc.), and access to instructor-only areas of the publisher’s website. At the focus group I attended it was clear that these supplemental materials take a lot of time (and thus money) to produce.

    In my own teaching I find many of these supplemental materials helpful. However, I wonder how widely used they are, and also how much they add to the cost of the book.

    Thus, I’m of two minds on the issue – on one hand I see my students spending >$100 on textbooks for my class and cringe, but on the other hand I can understand why the prices are so high.

    Note: The focus group trip mentioned above was paid for by the publisher, and I have also been paid for reviews of biology textbooks, so I’m not entirely free of conflicting interests here.

    (Edited to clarify Pharyngula's position based on his clarification post.)

    Thursday, January 08, 2004

    Bilbo Baggins immortalized in song

    A friend just IM'ed me a link with the following warning:

    Do you 1) have QuickTime installed on your computer, 2) have a low enough opinion of Leonard Nimoy that nothing could ruin him for you, and 3) like LOTR enough that whatever Leonard Nimoy did couldn't ruin that for you?

    If you say yes to all of those, and want a good laugh, go and enjoy The Ballad of Bilbo Baggins.

    I actually think the tune is rather catchy, though what dancing girls with brightly colored striped sweatshirts have to do with The Hobbit is beyond me. In the "things to note" category, keep an eye out for the button one of the women is wearing that says, "Elect Leonard Nimoy to the U.N." It's visible in the, er, shoulder shrugging scene.


    Here's the first post of my new blog. Hmm, what to say? Well, I think I'll just discuss who I am and why I'm starting this blog

    First, the who. I'm a full-time biology instructor at a California community college, and am currently untenured. In my teaching I prefer to focus on the biology of whole organisms, though I also enjoy delving into molecular biology and ecology/evolution. I've used many terms to describe myself professionally in the past, some of which are physiological ecologist, herpetologist, entomologist, and zoologist.

    I taught as an adjunct (part-time) instructor in another state before getting my current job, and unfortunately my SO remained in the other state to complete her work. So, for the past year and a half I've been divided between two states. The division is temporary, however, as we're currently in the process of selling our old house and will soon be moving all our belongings to California.

    Why am I writing this blog? No one reason stands out in my mind right now; it just seems like a good idea. I enjoy sharing information (probably a good thing for an educator), and my hope is that I can share and discuss topics of interest to me, on both a personal and professional level. I've read blogs for a short while, especially Dear_Raed's during the recent Gulf War, and have found them to be quite fascinating. So, I guess part of my motivation is that I feel that I've leeched enough and that it's about time I started contributing. And heck, it should be fun.

    Well, let's see where this thing goes ... enjoy!