Tuesday, August 31, 2004

First teaching day is done, along with some IMing

I gave my first lecture of the semester this afternoon, and after that had a great lab, even though setup for it finished barely before the lab started. Both class periods went exceptionally well, complete with lots of student participation, so it was an invigorating start to the semester. One big change from last semester was that I didn't have many petitioners, most likely because this is the first time my course has ever been offered. The old equivalent course (Zoology, which will be phased out) is still being offered, so I suspect most students just registered for that one even though we're now advertising my course as the one biology majors should take after cell biology.

I'm in the same lecture hall I was in last semester, but have 100 fewer students, so the atmosphere was friendly and unimposing, which was nice. I'm looking forward to having a smaller class again (though I never thought I'd describe a class of 60 as small).

As I've mentioned in the past, I use instant messengers to communicate with my students while I'm in the office; last semester I had more than 150 individual conversations over IM with students. However, I'm now discovering an unanticipated benefit: some students are keeping in touch long-term via IM. I've already had four instant messaging discussions with students so far this semester, and all of them have been with students from prior years.

This evening a student from nearly 3 years ago IM'd me just to chat. Back then I was teaching non-majors biology at another college in another state, so without IM's it's quite unlikely I would have ever heard from her again. This student was a returning student who was just beginning an elementary education program, and she's now about to start her teaching internship, so we chatted about the stresses of teaching preparation. Her daughter-in-law is now taking the same class I had this student in, and she wished I was still teaching there so her daughter-in-law could have me as an instructor. It was a great way to end a very good day.

Monday, August 30, 2004

Adventures of the lost fridge

The refrigerator in my teaching lab was ancient. The seals around the doors died years (if not decades) ago, and thus both the fridge and freezer kept filling with ice. It was so bad that the freezer was completely filled with ice, and I had to chip ice off the fridge insides monthly if I wanted to be able to close the door. We primarily used it to store formaldehyde preserved specimens, since it was completely unreliable for anything else.

Last week, however, I learned that another lab on campus was getting a new fridge. The fridge they were replacing was probably bought 20 years ago, but it was in great shape, and once I showed them the condition of my fridge they kindly offered to give me their old one for free. For some reason the maintenance folks decided the best time to do the fridge moving was 6am this past Saturday morning, so nobody was around when they did the switch.

I got in this morning to find the nice "new" fridge in my lab, but upon opening it discovered that the specimens that used to be in the old fridge were nowhere to be seen. Our lab tech was, understandably, rather concerned (though apparently not concerned enough to call the facilities people herself, since she had been in at least four hours by the time I arrived).

I quickly grabbed a cart, figured out where they'd taken the fridge, and ran off to try and save what I could, imagining the worst. I finally found the fridge in our campus facilities yard, standing against a wall in direct sun, complete with a small puddle of water under it. The sight was not encouraging.

I hesitantly opened the door, prepared to duel the armies of fungus and bacteria lurking inside, but to my surprise found that everything in the fridge was still cold! The secret to this mini-miracle was the freezer: even after two days in full sun it was still half full of ice, so it kept the rest of the unit cold. Let's all hear it for freezers full of ice!

So, in the end nothing too valuable was lost (though some algae samples have likely bit it), but this was definitely not how I anticipated starting the first day of my new semester.

RNC protests

There's a number of pictures from the Republican National Convention at Flickr (rnc tag, via BoingBoing). Appliance has a small collection of pictures of protest march signs, in case you missed seeing them live.

SC is back

Semantic Compositions has returned from his not-very-happy trip to Florida. Read all about it here.

Sunday, August 29, 2004

A new semester arrives tomorrow

Like many other bloggers in education, I start my fall semester tomorrow. I've got my faculty website updated, my course Moodle page ready to go, my first lecture and lab slides drafted out, and enough handouts copied for a small army, but even so I'm not nearly as prepared as I'd like to be (but then again I never am).

My nerves are starting to kick in, as I'm realizing just how much there's still left to do before my first lecture on Tuesday. One of the things that gets to me at this time of year is the sheer number of unknowns that I'm faced with: how many students I'll have, what they'll be like, how I should pronounce their names, whether the lecture room computer will still work, whether the online portion of my course will work smoothly, if I'll get enough student assistants to help with lab, and so on. It's even worse this semester as my entire teaching load is taken up by the new course I've designed, which includes three hours of lecture and three lab sections that are each six hours a week, and it's all a new prep. This is an incredible opportunity (certainly one that many young faculty members don't get), and it will be nice to do whatever I want whenever I want, but it's also quite intimidating.

I'm not making any major technological changes from last semester, though one difference is that I've dumped WebCT and will be using solely Moodle for the online portion of my course. Moodle seems more intuitive than WebCT, and I love that it's open source (see my comparison of the two here). I'll still be using the in-class response system; it was a resounding success last semester, and I might even start using it in lab if I can get another receiver for that room (see my reviews here, here, and here). Since I'll be working on lab design throughout the semester (translate: I haven't gotten all the labs written yet) I'm going to be posting labs online for student to print themselves, rather than having a printed lab manual.

As a side note, preparing new lectures and labs will take the majority of my free time this semester, so I may not be able to maintain regular posting. I'll try my best, though.

Saturday, August 28, 2004

Nothing brightens a day like kitten pictures

It's been one of those days where absolutely nothing seems like it can go right, and thus it was very nice to find that All The Stuff I Couldn't Fit in My AIM Profile had posted some new pictures of her incredibly cute kittens.
Kittens from Amanda at All the stuff I couldnt fit in my AIM profile

I want some cats, darnit. My SO and I have already built a six-foot-tall, four-shelf cat tree and purchased supplies for our future cats, but until our house construction is more complete it just doesn't seem to make much sense to get new pets.

Friday, August 27, 2004

Defining photosynthesis

Photosynthesis is a pretty miraculous thing. Organisms (most people think of plants) capture radiant energy from the great nuclear reactor in the sky and turn it into something they can use to do biological work. It's a fundamental part of life as we know it that's been studied for centuries, and thus you'd think most dictionaries and other places would have the definition of photosynthesis down pat.

Let's look at a few, starting with dictionary.com.
  • "The process in green plants and certain other organisms by which carbohydrates are synthesized from carbon dioxide and water using light as an energy source. Most forms of photosynthesis release oxygen as a byproduct." (from the The American Heritage® Dictionary of the English Language, Fourth Edition, 2000)
  • "The process in green plants and certain other organisms by which carbohydrates are synthesized from carbon dioxide and water using light as an energy source." (from the The American Heritage® Stedman's Medical Dictionary, 2002)
  • "The process of constructive metabolism by which carbohydrates are formed from water vapor and the carbon dioxide of the air in the chlorophyll-containing tissues of plants exposed to the action of light." (Webster's Revised Unabridged Dictionary, 1998)
  • Encarta's page on photosynthesis starts with, "Photosynthesis, process by which green plants and certain other organisms use the energy of light to convert carbon dioxide and water into the simple sugar glucose." (the article is quite long, and continues on to talk about other variations; this is just the first sentence)
  • A top 10 google-ranked page for "photosynthesis definition" (link; it was the first thorough non-dictionary link) provides this definition, "Photosynthesis is the conversion of carbon dioxide and water into a sugar called glucose using sunlight energy. Oxygen is produced as a waste product." (the rest of the text on the page discusses solely plants)
While these definitions share many features, one outshines the rest: they're all wrong.

The first glaring mistake in one of these definitions is the restriction to plants, since various species of Bacteria, Archaea, and Protista can also photosynthesize.

The primary problem with the definitions is that much of the biochemical information they specify is incomplete. All of the definitions include that the organisms take in carbon dioxide, yet there are numerous photosynthesizing organisms (primarily Bacteria) that do not use carbon dioxide as a carbon source, but still use light as an energy source. The prime example of this style of growth (termed photoheterotrophy) are purple nonsulfur bacteria, a family of bacteria that can use fatty acids, organic acids, amino acids, sugars, alcohols, and aromatic compounds (e.g. benzoate) as carbon sources in place of carbon dioxide. More commonly known is photoautotrophy, wherein organisms (e.g. plants) get their energy from light and their carbon from carbon dioxide.

Two of the definitions above specify that photosynthesizing organisms produce oxygen (and the others imply it by specifying water as a part of photosynthesis), yet oxygen production is not a common characteristic of all photosynthesizing organisms. This isn't even a terribly new observation, as the theory that photosynthesizing organisms always produce oxygen was first brought into doubt in 1883 by Theodor Englemann when he reported that purple sulfur bacteria appeared to be living solely on energy provided by the sun, yet did not produce oxygen.

Oxygen is produced by many photosynthetic organisms because they use water (H2O) as an electron donor. Photosynthetic organisms that don't produce oxygen (anoxygenic photosynthesizers) use some compound other than water as an electron donor. Hydrogen sulfide (H2S), thiosulfate (S2O32-), elemental sulfur (S0), and ferrous iron (Fe2+) can all be used by purple sulfur bacteria as electron donors, each potentially producing unique products. As an example, bacteria in the genus Ectothiorhodospira use hydrogen sulfide as an electron donor, and produce elemental sulfur as a product instead of oxygen (they typically live in salty aquatic environments).

So, if photosynthesis is not limited to plants, and doesn't necessarily include carbon dioxide, water, and oxygen, how is it defined? Here's one good definition:
"Photosynthesis is a series of processes in which electromagnetic energy is converted to chemical energy used for biosynthesis of organic cell materials; a photosynthetic organism is one in which a major fraction of the energy required for cellular syntheses is supplied by light." (Gest 2002)
By not focusing on the reagents used in one style of photosynthesis, this definition allows the full host of photosynthetic organisms, from bacteria to plants, to be included.

To be fair to the web, not all the definitions of photosynthesis out there are wrong. Here's a sampling of definitions I found that are pretty good (again starting with dictionary.com):
  • "synthesis of chemical compounds with the aid of light sometimes including the near infrared or near ultraviolet; especially : the formation of carbohydrates from carbon dioxide and a source of hydrogen (as water) in chlorophyll-containing cells (as of green plants) exposed to light involving a photochemical release of oxygen through the decomposition of water followed by various enzymatic synthetic reactions that usually do not require the presence of light" (from the Merriam-Webster Medical Dictionary, 2002)
  • "synthesis of compounds with the aid of radiant energy (especially in plants)" (Wordnet 2.0, 2003)
  • "Photosynthesis is a biochemical process by which the energy of light is converted into chemical energy in plants, algae, and certain bacteria." (Wikipedia)
  • The top google rank page for "photosynthesis" (link, link to page with definition) describes it as, "Photosynthesis is carried out by many different organisms, ranging from plants to bacteria. The best known form of photosynthesis is the one carried out by higher plants and algae, as well as by cyanobacteria and their relatives, which are responsible for a major part of photosynthesis in oceans. All these organisms convert CO2 (carbon dioxide) to organic material by reducing this gas to carbohydrates in a rather complex set of reactions." (the article continues on, going into extreme depth)
Gest, H. 2002. History of the word photosynthesis and evolution of its definition. Photosynthesis Research 73: 7–10. (pdf link)

Madigan, M., Martinko, J., and Parker, J. 2003. Brock Biology of Microorganisms. 10th edition. Prentice Hall, NJ.

Thursday, August 26, 2004

Link e-mailing and site feeds

I've got two site mechanics issues here:

1) The little envelope with an arrow on top that just appeared (next to the trackback link) will let you send a link to a specific post via e-mail. Happy e-mailing!

2) My Atom site feed is currently set to provide approximately the first paragraph (~255 characters) of each post, though I can also set it to provide the full text of each post. My question for my devoted readers is this: which would you prefer?
What kind of site feed would you prefer here at Rhosgobel?
Short feeds
Full-post feeds
It doesn't matter to me
Free polls from Pollhost.com

[Update 09/07/2004: Poll has been stopped; the results are posted here].

Photosynthesis Treasure Trove

Dr. Govindjee, a professor emeritus at the University of Illinois at Urbana-Champaign, has a website full of information on photosynthesis (which makes sense considering that he's world-renowned for his work on it, including 389 publications to his name).

His "Celebrating the Millennium: Historical Highlights of Photosynthetic Research" pages (part 1, part 2, and part 3) each contain dozens of full-text PDFs from Photosynthesis Research discussing the topic throughout the last century, and his teaching resources page is full of links. If you're at all interested in reading up on photosynthesis, Dr. Govindjee's website is the place to go.

I've already read a few of the Historical Highlights articles, and once I get time to sit and read I plan on perusing a whole bunch more of them.

Wednesday, August 25, 2004

Semantic Compositions Update

I just got a short e-mail from Semantic Compositions. SC's great-uncle died today in Florida, and SC is now helping with funeral preparations. He doesn't expect to be back in town until this coming Sunday or Monday.

Tangled Bank #10

Tangled Bank Blutton
This week's edition of the Tangled Bank has been posted by Wolverine Tom. This edition sounds quite impressive, as it has "8 articles that highlight the best of science throughout the blog world."

How I fell for Niagara, part 2

And now for the second of my two posts on Niagara Falls (the first post is here):

Lewiston and 18F:

On Saturday we traveled north from Niagara Falls, heading for Old Fort Niagara, and stopped along the way in Lewiston for lunch. Lewiston has a main street a few blocks long, lined with shops and restaurants; the picture below was taken on Saturday afternoon:

Niagara Falls area - Lewistown main street

After lunch and a bit of shopping (including a visit to a bookstore that had fewer books on display than I have in my house) we headed north to Old Fort Niagara. We took 18F, instead of the Parkway, and were glad we did. 18F starts in Lewiston, and for most of its length is a two-lane road lined with classic northeast-style houses and lush, green foliage. The road travels along the shores of the Niagara River, so we got river vistas every now and then. There weren't a lot of cars or tourists around, which made the drive and the towns even more appealing.

Niagara Falls area - 18F
The picture above was taken along 18F, between Lewiston and Youngstown.

This leads to my second recommendation for the Niagara Falls area: if you want to do something different, look for a good bed and breakfast or small hotel near either Lewiston or Youngstown. Both are small towns that seem like they'd be nice to spend a relaxing weekend in, yet are close enough to Niagara Falls that you could drive there in less than 20 minutes. Note, of course, that I didn't stay in either town, so you may want to take this recommendation with a very large grain of salt.

A highlight on the drive north from Niagara Falls was Whirlpool State Park, which overlooks a region of the Niagara River where the water flows in a circle: for half the width of the river the water actually flows upstream. This park was nearly empty when we were there, but was definitely worth the visit. Below you can see a view from Whirlpool State Park, looking up the Niagara River towards the falls.

Niagara Falls area - view from Whirlpool State park

Old Fort Niagara and the Ft. Niagara Lighthouse

Old Fort Niagara is on the shores of Lake Ontario and was originally started by the French in the late 1600s. The earliest outposts were abandoned until 1726, when the French built a large "castle" on the site. The fort changed hands to the British in 1759 (where it served as a British fort during the Revolutionary War), was transferred to the US in 1796, was taken by the British again in the War of 1812, and was finally given back to the US at the end of the War of 1812.

Old Fort Niagara front

What is fascinating about this fort is that you can get a taste of what military life was like during three different periods of life in North America. The French castle and dirt walls on the site were built around 1726, the redoubts (towers) and many other buildings were built by the British during their first occupation (fortifying in anticipation of an American revolutionary assault), and the Americans modified it again during the Civil War. Thus in this one fort you can explore early French colonial architecture, British colonial military architecture, and American Civil War military architecture. It's a fascinating exercise in exploring the effect of technological development on military construction, and is a marvelous location for D&D players to see a real-life counterpart of their gaming worlds.

Niagara Falls area - Old Fort Niagara Lighthouse

Just outside the fort is the Fort Niagara Lighthouse, built in 1871. The lighthouse doors were open when we drove up, and we discovered that they were leading guided tours to the top of the lighthouse. I signed up (it was free, but I had to sign a waiver) and then climbed more than 70 steep, narrow stairs to the top of the lighthouse. The lighthouse was missing its lens, but the view from the top was extraordinary, and it was thrilling to be able to climb up an actual lighthouse staircase (I've always loved to look at lighthouses, but had never been able to climb up one before). To give you an example of just how steep and narrow the stairs were, here's a picture of the stairs leading down from the top, with one of my fellow adventurers attempting to get through the tiny door:

Niagara Falls area - Old Fort Niagara Lighthouse door down Niagara Falls area - Old Fort Niagara Lighthouse stairs

This thus leads to my third recommendation for the Niagara Falls area: if you have an extra afternoon while you're in the area, a trip to Old Fort Niagara is well worth the time, and if the Fort Niagara Lighthouse is open while you're there, take a few moments and climb to the top. Both were well worth it, and were definitely highlights of my trip.

Tuesday, August 24, 2004

New Abu Ghraib Report

An independent commission's report on the Abu Ghraib prisoner abuse was released today (the commission was created by Rumsfeld in May) . There's a DOD article here, a PDF of the full report, and a full transcript of the commission's press conference. Here' s a few snippets I found noteworthy in the press conference:
  • "Through our investigation and review, we found a string of failures that go well beyond an isolated cell block in Iraq. We found fundamental failures throughout all levels of command, from the soldiers on the ground to Central Command and to the Pentagon. These failures of leadership helped to set the conditions which allowed for the abusive practice to take place. " - Former U.S. Representative Tillie Fowler (R-Fl)
  • "None of the targets in the photos [released in April] were there because of presumed valuable information. There were cases at Abu Ghraib of abuse directed at intelligence targets, but none of them were photographed." - Former Secretary Of Defense James R. Schlesinger
  • "There was no policy of abuse; quite the contrary. Senior officials repeatedly said that in Iraq, Geneva regulations would apply." - Schlesinger
  • "There are now some 300 cases, more or less, of abuses being investigated, many of them beyond Abu Ghraib. So the abuses were not limited to a few individuals." - Schlesinger
  • "A degree of responsibility for failure to provide adequate resources to support the custodial and intelligence requirements throughout the theater and also for the confusion about permissible interrogation techniques extends all the way up through the chain of command to include the Joint Staff of the Joint Chiefs and to include the Office of the Secretary of Defense." - Former Secretary Of Defense Harold Brown

Monday, August 23, 2004

Some links

I've spent most of the day on the couch since I'm somewhat sick (great timing, eh?), so here's an assortment of links I've been saving for one reason or another.

Semantic Compositions

SC and Mrs. SC both rushed off to the airport this morning to fly to Florida so they could be with his ailing great-uncle.

SC has temporarily stopped blogging as he travels. He may be able to make updates from the road, though he has also indicated that he may try to send updates through me here at Rhosgobel. I have not received any news since before he left, but if I receive more information I will post it as soon as possible.

I'm sure that SC would appreciate any kind words you have to send.

Tangled Bank #10 coming soon!

Tangled Bank Blutton
The next edition of the Tangled Bank will be hosted by Wolverine Tom. Be sure to send Tom a recent biologically-related post so that he can highlight it this coming Wednesday.

Sunday, August 22, 2004

How I fell for Niagara, part 1

While deciding where to drive on our recent cross-country trip, my mom pointed out that Niagara Falls was only a few miles away from I-90 in New York, the route we'd be taking to Albany. Since I had never been to Niagara Falls, and my mom hadn't been there for decades, we decided to stay in the town for two nights.

Niagara Falls is a large waterfall on the Niagara River, near Buffalo, New York. The river connects Lake Erie and Lake Ontario, and also serves as the border between the United States (on the eastern shore) and Canada (on the western shore). The falls are visible from both countries.

My mom had never been to the Canadian side of the falls before, and we considered heading into Canada to see them from that side. In the end we decided that traveling across international borders with a car full of my mom's household possessions was probably asking for trouble, so we stayed on the New York side the entire time.

Niagara Falls, the city:

Before arriving in Niagara Falls, I imagined that the city was probably a moderately sized thriving tourist town, full of tree-lined streets, and cute shops, much like Victoria, B.C., which I had visited earlier in the summer. Instead, the town seemed like it was relatively economically depressed, which was sad since the area clearly brings in tons of tourists.

Our five-story hotel was a few blocks from Niagara Falls State Park, in a reasonably nice area that looked like it was probably built up in the 1960's. The hotel's thin walls let us hear the neighboring room's kids until 2am, and it only had one small elevator and two stairways to service its five stories. The area directly around our hotel was filled with other hotels and a few small restaurants, but very few stores. I had hoped to find a nice coffee shop to sit and read in, but didn't see any near the hotel.

After unloading the car we set out to find a restaurant and a bookstore. Along the way we ran into two closed roads (and the next morning found a third). The roads were just blocked off with "Road Closed" signs, and did not have detour signs or any notice about when they'd be reopened.

Niagara Falls road closed

This leads to my first recommendation for anyone traveling to Niagara Falls, NY: bring an excellent quality map of the downtown area. The AAA Buffalo map has a good map of downtown Niagara Falls, but don't rely on the AAA New York state map, it's far from adequate.

The shopping areas of downtown Niagara Falls looked like they had once been quite nice, but many stores seemed like they hadn't been renovated in years, there was almost no foot traffic along the streets, and scattered shops were even boarded up.

Niagara Falls store

Little Italy, a region of downtown Niagara Falls, showed scattered signs of its Italian heritage (Gianni's restaurant, Di Camillo bakery), but was virtually empty on the Friday evening we were there. Near Little Italy we found an excellent Italian restaurant, Fortuna's (827 19th, in Niagara Falls, NY), that seems to date back to the days when Little Italy was thriving. The restaurant was populated mainly with locals, had excellent food, and as we ate at least four parties being shown to tables stopped and greeted other patrons of the restaurant.

We never did find a bookstore.

Niagara Falls State Park:

I got my first view of the falls as night was falling on Friday evening; they were massive and awe-inspiring. What surprised me was that instead of being at the bottom of the falls, the viewing areas are up at the top, so I could walk right up to the edge and watch the water roll over.

What was interesting that first night was the contrast between the American and the Canadian sides of the falls. Niagara Falls, Ontario is visible across the river from the New York side, and the Canadian town looks as though it's pulsating with life. There are at least 10 high-rise hotels (whereas there are no high-rise hotels on the US side), wide boulevards filled with light and flashing signs, and restaurants seemingly everywhere (and, in our imaginations, a bookstore on every corner).

Niagara Falls at night, white Niagara Falls at night, colored

Niagara Falls State Park is a huge park with exquisitely maintained facilities. It was a wonderful place to explore the falls from, and is a must-see if you're visiting the area. One of my favorite places was Goat Island, an island in the middle of the Niagara river; we drove onto the island and were able to get extremely close-up views of the falls.

Here are a few more pictures of the falls, including a picture of the very edge, which I was only a few feet away from at the time (in the edge picture you can also see a "Maid of the Mist" boat at the bottom of the falls).

Niagara Falls rolling water Niagara Falls edge with boat visible

As expected, there were a tremendous number of tourists from all over the world visiting the park, which made it a great place to sit and people-watch. This gentleman in his saffron-colored clothes caught my eye:

Niagara Falls area - gentleman with saffron robes taking a picture

Here ends part one of my two-part Niagara Falls post. Be sure to stay tuned for the second (and final) installment, wherein I tour more of the Niagara Falls area, including an eighteenth-century fort and a nineteenth-century lighthouse.

[Update 8/25/04: The second installment has been posted.]

Saturday, August 21, 2004

So I'm slow ...

I'm finally getting around to reading the backlog of Pharyngula that I missed during my cross-country trip, and found this:

giant stuffed microbe dolls ... I want them all!

Giant, plush microbes. They are SO cute. They've got representatives from most kingdoms: Bacteria, Fungi, Protista, and Animalia (they even include some viruses). You can get a set of 15 for $75 ... I am very tempted. Seeing as I'm going to be teaching a few labs on microbial diversity, I should be able to count this as a professional expense, no?

Oh, maybe I can buy these "microbial models" with my department's (non-existent) budget!

Gmail helper apps

There's a number of new tools out there to help users of Gmail. Google has released a Gmail notifier application that lets you know when you have new mail. The Gmail Wiki and Mark Lyon also have a host of Gmail related applications that folks have developed. If I didn't already use Outlook for much of my mail, I'd install one of the "mailto:" handlers.

(via BoingBoing; I was going to try to include this in my earlier BoingBoing based post, but it just didn't fit.)

Friday, August 20, 2004

Doctors and Torture

Both The Lancet and New England Journal of Medicine have published articles looking at the role of military personnel in torture.

Doctors and Torture, an article in the New England Journal of Medicine, looks at the role US Military doctors played in the torture of prisoners at Abu Ghraib, medical misdeeds at Guantanamo Bay, and the conflict doctors can face in the military.

Abu Ghraib: its legacy for military medicine (registration required) is a scathing article in The Lancet that goes further than "Doctors and Torture" in detailing the abuse and misdeeds of medical personnel, as well as making a stronger call for reform. Here's a few excerpts:
  • "In one example of a compromised medically monitored interrogation, a detainee collapsed and was apparently unconscious after a beating, medical staff revived the detainee and left, and the abuse continued."

  • "In one example, soldiers tied a beaten detainee to the top of his cell door and gagged him. The death certificate indicated that he died of "natural causes . . . during his sleep." After news media coverage, the Pentagon revised the certificate to say that the death was a "homicide" caused by "blunt force injuries and asphyxia.""

  • "Legal arguments as to whether detainees were prisoners of war, soldiers, enemy combatants, terrorists, citizens of a failed state, insurgents, or criminals miss an essential point. The US has signed or enacted numerous instruments including the UN Universal Declaration of Human Rights, the UN Body of Principles for the Protection of All Persons under Any Form of Detention or Imprisonment, UN Standard Minimum Rules for the Treatment of Prisoners, the Convention Against Torture and Other Cruel, Inhuman, or Degrading Treatment or Punishment, and US military internment and interrogation policies, collectively containing mandatory and voluntary standards barring US armed forces from practicing torture or degrading treatments of all persons."

Both of these articles' discussion about how otherwise normal doctors can become complicit with torture and other atrocities remind me of Milgram's classic studies regarding obedience to authority. I can still remember seeing a video of Milgram's study, and reading his papers, in my social psychology class when I was an undergrad; they drove home the point that the majority of people will blindly obey an authority figure, even if it involves killing someone. This tendency to blindly obey authority is why we need strongly enforced policies in place to prevent abuse and torture.

(Both articles via BoingBoing)

It's like Watership Down

CNN (via Reuters) has an article about a Brazilian tribe, the Piraha, whose language lacks most words for numbers.
"Their words for numbers appear limited to "one," "two" and "many," and the word for "one" sometimes means a small quantity.

"There is no word for 'number', pronouns do not encode number (e.g., 'he' and 'they' are the same word), and most of the standard quantifiers like 'more,' 'several,' 'all,' 'each' do not exist," Gordon wrote.

This reminds both my SO and I of Watership Down, wherein Lapine (the rabbit language) uses the word "hrair" to describe any number over four.

An interesting point in the article was that while adults had significant problems working with large numbers, children of the tribe did not. This seems to imply that the language itself may be inhibiting the mental abilities of its speakers to count. I wonder what limitations English has ...

Well, I've played enough at being SC for today ([Yeah, and you weren't even that good at it --ed.]).

Thursday, August 19, 2004

Some tools for field lab planning

I've managed to get my fall lab schedule back in order, though I don't think it'll ever be as perfect as when I had lab scheduled for Thanksgiving day. Now I just need to sit down and formally write-up (or find existing labs for) the new labs I'm going to be doing.

While working on the schedule I found two sites that helped me plan my field labs:

Sunsetsunrise.com creates monthly, printable, calendars for cities across the world listing the daily sunrise, sunset, and twilight times.

The NOAA CO-OPS site has an excellent tidal predictions page that covers the entire United States.

My first comment spam

I just got my first piece of comment spam (in this thread). Whee.

What's somewhat odd, however makes perfect sense now that Pharyngula has explained it to me, is that my hit-counter didn't record a visit during the time the comment was left.

Wednesday, August 18, 2004

Just when I think I have it all figured out ...

That darn Thanksgiving holiday comes in and ruins everything.

I thought I had my fall lab schedule all set, with everything fitting perfectly. I'd managed to get all the phyla of protists and animals introduced before our field trip to the intertidal zone (which is occurring inconveniently early, but it's not like I can control the tides or anything), and I'd fit two long-term rearing experiments into the last few weeks of the semester.

Then, this afternoon, I looked at the calendar and realized that I'd scheduled three labs to take place on Thanksgiving day. One of the labs was to check bacterial cultures that had been started earlier in the week, and another was to check plants that had been planted the week before.

So, now it's back to the drawing board to reschedule the entire end of the semester. Sigh.

Why have I only found this site now?

The Wage Slave Journal has an extremely detailed Scorecard of Evil for George W. Bush. The scorecard lists, in chronological order, all the various questionable things the Bush administration did in its first three years in office. The scorecard sadly ends in October of 2003, but it's still a great read.

I'd nearly forgotten some of the things that happened in the early days of the Bush administration:
  • 3-20-2001: Bush signs ergonomics repeal. [and on 4-05-2002 suggested voluntary rules to replace them.]
  • 4-12-2001: Bush tries to cut birth control coverage for federal workers.
  • 5-8-2001: Bush cuts funding to anti-nuclear proliferation programs.
  • 5-20-2001 & 7-26-2001: Bush rejects a protocol to enforce germ warfare treaty.
  • 6-15-2001: Bush denies Africans AIDS drugs through international aid agency.
  • 8-8-2001: Bush eases Clinton rules on industrial pollution.
  • 8-28-2001: Bush delays reparations to cancer-stricken uranium miners.
  • 11-2-2001: Bush overturns the 1978 Presidential Records Act.
  • 1-15-2002: Bush relaxes environmental rules on wetlands development.
  • 1-15-2002: Bush plans to store--rather than destroy--nuclear weapons slated for reduction.
  • 1-22-2002: Bush backs drilling for natural gas in national monument.
  • 2-24-2002: Bush makes taxpayers--rather than polluters--pay to clean up Superfund sites.
  • 2-26-2002: Bush tells welfare mothers to find husbands.
  • 3-29-2002: Bush uses alternative energy funds to pay for printing energy policy.
  • 4-26-2002: Bush lets mining companies dump waste into streams.
  • 5-23-2002: Bush reopens mining on proposed national monument.
  • 6-12-2002: Bush shields missile defense plans from congressional oversight.
  • 6-14-2002: Bush refuses to enforce an important provision of the Clean Air Act.
  • 6-19-2002: Bush says toxic sludge is good for fish.
  • 7-1-2002: Bush cuts funds to Superfund cleanup sites.
  • 7-16-2002: Bush creates a program for Americans to spy on each other.
  • 7-29-2002: Bush praises miners' rescue while cutting the budget for the department that saved them.
I could go on, but I'll stop here, since the real power of the list is simply the sheer number of things that the Bush administration has done that are ethically questionable.

What if we had a president in office who did the exact opposite of everything on this list? Let's imagine ...
  • 3-20-2001: Bush enforces ergonomics regulations. [and on 4-05-2002 suggests additional protections for workers.]
  • 4-12-2001: Bush increases birth control coverage for federal workers.
  • 5-8-2001: Bush increases funding to anti-nuclear proliferation programs.
  • 5-20-2001 & 7-26-2001: Bush accepts a protocol to enforce germ warfare treaty.
  • 6-15-2001: Bush helps provide funding for AIDS drugs for Africans through international aid agency.
  • 8-8-2001: Bush enforces rules regulating industrial pollution.
  • 8-28-2001: Bush quickens reparations to cancer-stricken uranium miners.
  • 11-2-2001: Bush enforces the 1978 Presidential Records Act.
  • 1-15-2002: Bush strengthens environmental rules on wetlands development.
  • 1-15-2002: Bush plans to destroy--rather than store--nuclear weapons slated for reduction.
  • 1-22-2002: Bush prevents drilling for natural gas in national monument.
  • 2-24-2002: Bush makes polluters--rather than taxpayers--pay to clean up Superfund sites.
  • 2-26-2002: Bush helps welfare mothers get job training and childcare.
  • 3-29-2002: Bush uses alternative energy funds to promote alternative energy.
  • 4-26-2002: Bush prevents mining companies from dumping waste into streams.
  • 5-23-2002: Bush prevents mining on proposed national monument.
  • 6-12-2002: Bush opens missile defense plans to congressional oversight.
  • 6-14-2002: Bush enforces an important provision of the Clean Air Act.
  • 6-19-2002: Bush says toxic sludge is bad for fish.
  • 7-1-2002: Bush increases funds to Superfund cleanup sites.
  • 7-16-2002: Bush doesn't create a program for Americans to spy on each other.
  • 7-29-2002: Bush praises miners' rescue while increasing the budget for the department that saved them.

Tuesday, August 17, 2004

Diversity labs

I'm starting up a new course this fall, and it's finally time to make all the nitty-gritty decisions about exactly which labs get run and when, and what will occur in each lab.

It's one thing to say, "I want to have a lab that introduces the kingdoms (or protists, or plants)," and it's quite another to actually find said lab. Most of the labs I've seen haven't been ideal. Many read like a mediocre textbook and are simply glorified lists of facts about each group of organisms within the lab's chosen taxon. The only student work in these labs is usually to sketch a given set of organisms (usually on slides or in biomounts), label their sketches or pre-prepared sketches, and in the process learn a large number of anatomical terms and life cycle details about the organisms they're "observing".

While students can benefit from sketching organisms and reading selected details about the group of organisms they're exploring, these labs require no critical thinking, and are usually dreadfully boring. Most of the lab manuals I've looked through have at least seven or eight labs built in this style as they march through the lineages of all the kingdoms.

What I'd like to see more of in these labs are components that require critical thinking and active exploration on the part of the student. Instead of simply listing the characteristics that differentiate the taxa, why not show students the organisms in each taxa and have them try to figure out what differentiates them? Even if the students flounder and don't come up with the ideal characteristics, they'll have spent an hour or more critically examining the organisms in the lab room, and it should be easy for an instructor to lead an end-of-lab discussion on what the actual defining characteristics of the group are, including some relevant anatomy and life history lessons.

Thinking along these lines I've been working on designing the first lab of the semester. My primary goal is to introduce some basic information about the currently accepted domains and kingdoms, preparing the students to explore each kingdom in more detail later in the semester. Secondary goals are to introduce the ideas of taxonomic classification, expose the students to organisms they may not have seen before, and have an interactive lab where the students get to move around and meet their peers.

I've come up with a few basic ideas that could work for the lab. The first assumes the students do not know what all the kingdoms of life are (not a bad assumption, in my experience), and the remainder assume the students have had some recent introduction to the topic.

1) Randomly position organisms representing each kingdom around the room, without any labels other than a species name or a number. The primary task during lab for students would be to group the organisms into kingdoms, and in doing so determine what makes the kingdoms different from each other. Probably the easiest way to run the lab would be to have groups of students quickly sketch each organism onto a card, and then sort the cards into groups on their lab tables.

2) Place organisms from each kingdom on a separate table (e.g. table 1 is animals, table 2 is plants, etc.). The students' primary task during lab would be to determine the similarities between all the organisms within one kingdom (table), and then determine what differentiates each kingdom from the other kingdoms.

3) This starts out the same as number two (each kingdom is on a different lab table), but instead of labeling each table with the kingdom name, the tables are left unidentified and it's up to students to first figure out which kingdom is at their table, before continuing with the rest of the lab as described above. For some tables it will be obvious (*cough*animals and plants*cough*), but for others it could be a challenge.

4) Distribute organisms from the different kingdoms randomly around the room, but since students have been introduced to the kingdoms already, their task would be to determine which kingdom each organism belongs to. This could be done either by giving the students keys and having them key out each organism, or by having them try to determine the answer based on material that has been introduced previously (e.g. basic characteristics of each kingdom as discussed in lecture). My preference would probably be the latter, since using keys can get very mechanical, though exposure to keys is important.

All of these options would end with a class discussion wherein the actual characteristics of the kingdoms would be introduced, along with some of the basic biology of each kingdom.

The main problem with the first option is that it requires that the students not come in with recent knowledge about the kingdoms. Since I have lecture before lab I will almost certainly be lecturing about the domains of life then, and preventing myself from talking about the kingdoms in that lecture would be awkward.

For now I'm leaning to the third option (kingdoms divided by table, but left unidentified initially), possibly including some unidentified organisms on the side of the room so students can test the effectiveness of their chosen characters.

Monday, August 16, 2004

Yet more proof that insects are cool

(Or: A look at bee pheromones)

Let's say you and your family are living in a nice home that you've built from the ground up with your own sweat and tears, and then all of a sudden some punk kids come around the corner and start pelting your home and family members with rocks. What would you do? You'd grab all your buddies and rush those punk kids to scare 'em off.

Well, that's exactly what some bees did recently in Santa Ana after a few kids started throwing rocks at the hive the bees had built in an apartment complex wall. What the kids didn't expect, however, is that the hive contained an estimated 120,000 bees, 40,000 of whom were found inside the hive while the other 80,000 were out foraging (or defending the hive) at the time and were only caught later (LA Daily News, LA Times, CNN). The hive weighed more than 500 pounds. When firefighters arrived on the scene they tried to hold the bees off with water but were unsuccessful (seven firefighters were stung, according to the LA Times), and everyone had to wait for professional beekeepers to arrive before the bees were finally "controlled".

Bees are an amazing example of a social insect, and there's a lot of neat biology contained in this little event. Probably the most interesting, though, is how 120,000 bees were able to communicate with each other and coordinate a multi-hour defense of their hive without cell phones, radios, GPS systems, or verbal or print-based communication of any kind.

Bees communicate primarily through pheromones, which are organic molecules released by one individual that affect the behavior or physiology of another individual. Moths are a good example of an animal that uses pheromones: male Bombyx mori moths (silkworm moths) respond behaviorally to one molecule of female Bombyx mori pheromone (bombykol) in 10^17 molecules of air. The males, of course, are trying to find females so they can mate, and pheromones help a lot when individual moths may be miles apart.

Bees use pheromones to coordinate virtually all of their hive activities, including mating, kin recognition, defense, orientation (to food, nests, and swarms), and many colony-level functions (maintenance of nectar stores, inhibition of worker bee ovaries, inhibition of queen rearing). More than 18 individual pheromones have been identified, and it's hypothesized that more than 36 exist (note: this information comes from a 1987 bee book, so is probably out of date).

The firefighters and other people around this particular bee colony should have been most concerned with the alarm pheromones of the bees. Bees produce multiple alarm pheromones, one of which is isoamyl acetate (the first to be discovered; others include 2-nonanol, (Z)-11-eicosen-1-ol, and 2-heptanone). Isoamyl acetate can be released by bees voluntarily, but is also released involuntarily when a worker bee stings.

When bees sense alarm pheromone in the air around them, they immediately begin showing defensive behaviors. If alarm pheromone is put onto a marble that is rolled into a hive entrance, the bees become more agitated, assume aggressive postures (the bee equivalent of "grrrr"), and once they determine that the alarm pheromone is coming from the marble, they'll charge the marble and group around it, evaluating the threat that it poses. If the marble stays put they generally won't try to sting, but if the marble moves the bees will begin stinging.

Alarm pheromones also act as an orientation pheromone, meaning that bees can follow the gradients of alarm pheromones in the air to determine the point source of the pheromone. Thus, as soon as one bee has stung an object, that object is tagged as a threat and all surrounding bees can use the alarm pheromone released by the bee's stinger to find the location of the threatening object.

So we now can understand how the bees were defending their hive. Betsy and Barbara Bee, along with some of their sisters, were stationed as guards at the entrance to the hive. When the kids rounded the corner, Betsy and Barbara had just gotten back from sipping some honey during their break, and were focusing on releasing Nasonov pheromones (involved in orientation) to ensure that all the foraging worker bees would be able to find their way home. As soon as the kids started to hurl rocks at the hive, however, Betsy and Barbara both started voluntarily releasing alarm pheromone. This alarm pheromone alerted the bees in the hive that there was some danger at the entrance to the hive, and thus they began to congregate around the hive entrance. Betsy, Barbara, and their sisters then began to search for the source of the danger, focusing on anything that moved near the hive. Since they were already pumped up on alarm pheromone, once they found something that was moving (e.g. a human flailing wildly at them) they stung it, which released more alarm pheromone, which then caused more bees to become aggressive and fly towards the person they had just stung. Since the pheromones persist in the atmosphere even after the bees have stung, newly arriving bees immediately knew that there was a threat, and even knew who specifically their sisters had determined was posing the largest threat.

Betsy and Barbara, along with 119,998 of their sisters, died valiantly defending their home.

Note: Some reports have stated that there were three hives, not one, in the wall. I've written this as though there were one hive to simplify things.

Sunday, August 15, 2004

June 18, 2004: Hourly Pictures

Today was our last full day with my colleagues, and it began with an extended hike around the island. My SO and I were determined to try to photograph (and catch) some of the few grasshoppers that we had been hearing and seeing on the island, so we kept hanging back from the group to try to spot them. Eventually we heard some from afar in a large open area, so we told the rest of the group to go on ahead while we hunted. We ended up spending at least 30-45 minutes tracking the grasshoppers before we finally got close enough to photograph them, since they were incredibly cryptic, and when they flew it was often for a very long distance (we watched one fly 200+ feet before entering a stand of trees).

After lunch the other members of our group decided to take yet another trip to yet another island, but my SO and I were exhausted from the busy week and decided to stay behind to spent the afternoon reading and sleeping. We woke up just as the group was returning, walking like zombies up the dock platform. That night I sorted through my pictures and gave a "best of the island" picture show.

Today has some of my favorite hourly pictures from the trip. The driftwood textures (1200) came out as I'd hoped, and my picture of the sunset through the trees (2100) is my favorite recent sunset picture.

Today also has a good example of the tides in the area: the 1300, 1815, 1910, and 2100 pictures are all of the same location (though with varying camera angles). This little bay used to house the dock for the island, so at low tide the island was inaccessible.

Last, look at the 1100 picture to see some of the lichen 'forests' that were growing on the island. Lichens are slow-growing creatures that are mutualists, a combination of a fungus and either an alga or a cyanobacterium (depending on the species). Typically (in the southwestern US, at least) lichen are found in thin layers on rock, so I was excited to find them growing in carpets 2-4 inches high over much of the island.

Our hourly pictures from the day are below. (This text was written after returning from the trip).

06-18-04: 0815 Posted by Hello

06-18-04: 0900 Posted by Hello

06-18-04: 1000 Posted by Hello

06-18-04: 1100 Posted by Hello

06-18-04: 1200 Posted by Hello

06-18-04: 1300 Posted by Hello

06-18-04: 1400 - Reading
06-18-04: 1500, 1600, & 1700 - Sleeping

06-18-04: 1815 Posted by Hello

06-18-04: 1910 Posted by Hello

06-18-04: 2030 Posted by Hello

06-18-04: 2100 Posted by Hello

06-18-04: 2200 - Picture show / talk in progress

06-18-04: 2245 Posted by Hello