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Steven D. Brewer's blog

Project at BioQUEST

June 20, 2008 by Steven D. Brewer

This time, I decided I was interested in working on learning how to build models related to invasive species and Garlic Mustard. I spent a lot of the day yesterday struggling with the linear algebra of population models. When I went to bed last night, I decided I was making things too difficult for myself and, this morning, I realized I could implement it quite simply using a spreadsheet. When I came in this morning, I sat down and sketched it out. It turned out to be quite simple to implement a Lefkovitch model -- I still don't really get the linear algebra, but maybe that's not necessary.

There are 3 or 4 other people working on the invasive species project with me. We're trying to develop some investigative cases that will lead students to conclude that they need a model to make predictions about what's happening. We also are working on building a set of directions that students can use that aren't too directive for making a Lefkovitch model. Finally, I'm interested in building a netlogo model to look at the relationship between disturbance and invasive species.

Tomorrow, we'll finish our curriculum development project and present it. On Saturday, I'll start driving home.

My injuries are much better. Today, I can walk, rather than hobble. I still haven't really been successful at riding my bike, but I'll probably give it a try again this afternoon. The first time I tried, I couldn't get my foot in the pedal. The second time, I managed to get my foot in the pedal, but I couldn't make it go around without standing up in the pedals. Maybe today will be the charm.

STL -> Cape Girardeau

June 19, 2008 by Steven D. Brewer

SciencoIn spite of my knee, I went to the Botanical Garden and hobbled around for an hour after lunch. It was wonderful. I've always loved the garden and wish I could visit it every week or two and really learn to recognize all those plants.

We finished up in St. Louis around 2pm and headed on to Cape Girardeau. It was a couple hours drive south, through increasingly old terrain. We arrived and were installed in dorm rooms. The last time, I stayed in a dorm, it was pretty comfortable. This place is pretty bare bones. The shower is so small, I can barely turn around. At the hotel in St. Louis, they gave me 4 pillows per bed -- here, you get one pillow and you have to make the bed yourself. At first, I couldn't get the air conditioning to work, but eventually got it to cool off and slept pretty well.

In typical BioQUEST fashion, we're to form groups today and pursue a short project to be presented tomorrow morning. I have a number of ideas for things I might want to do, but there's not time to do very much. And I'm not inclined to spend all my time working on the project either.

Link Clouds with Wordle

June 16, 2008 by Steven D. Brewer

I saw a reference to wordle which can build link clouds based on a text. I constructed this one based on the text I've been writing from my talk at NCSU. I thought it looked pretty.

BioQUEST begins

June 15, 2008 by Steven D. Brewer

I made it to BioQUEST yesterday. At the hotel in the morning, I checked that I could actually attend to my personal needs (like putting on shoes and socks) and, after a quick breakfast with Phil and Jackie, I got in the car and drove to St. Louis. I'm still not very mobile, but I can hobble around enough to survive.

After introductory remarks, I participated in a session on developing a problem-space in desiccation tolerance for teaching advanced techniques in plant biology. The approach one scientist is using involves constructing phylogenomic trees to see whether genes involved in desiccation were recruited from stress pathways or seed/pollen pathways. There was a parallel session on GIS. After dinner, there was a talk about cassava and ongoing attempts to improve the cassava plant to make it a more attractive crop. Cassava has been neglected because, although its very widely cultivated, its mainly used by poor people who don't participate in the money economy and, therefore, it doesn't have big economic impacts the way rice or corn does.

Today, we finish up at the Botanical Gardens and drive south to Cape Girardeau where we'll be for the rest of the workshop.

Whoops!

June 15, 2008 by Steven D. Brewer

Whoops!Phil and I took a longish ride today to Meadowbrook Park. On the way back, I took a spill onto the pavement. My wheel dropped into a rough spot in the pavement and I lost my grip on the handlebars. The pavement came up quick and I ended up on my back in the road. Phil asked, "Are you OK?" I responded "No!" I got Phil to pull the bike off me, which had gotten tangled up with my leg and, by then, I'd decided that I wasn't going to die immediately. I managed to get up enough to move to the edge of the road and then rested in the grass. Phil called Jackie and she and Lucy came to get me with the cool car.

I've got a lot of bruises, but don't seem to have broken anything. I've smashed up my knee pretty bad, but it can take my weight, so I don't think there's anything seriously wrong with it. I don't think I'll be riding my bike for a few days though. Amazingly enough, my bike seems fine -- just a scrape in the coating on the lock.

Everyone helped me get home, brought me ice packs, ibuprofen, and a good, strong drink. After resting for a bit, I'm up and about, in a manner of speaking. I'm hoping I'll still make it to BioQUEST tomorrow, but I don't think I'll really know until I go to get up tomorrow morning.

Bicycling

June 13, 2008 by Steven D. Brewer

I haven't done a huge amount of bicycling since I've been in Champaign, but I think I've gotten out every day. Some of the days I rode here, but for the past couple of days, we ended up leaving bike or bikes here, driving over, and then going out on rides.

On Thursday, we rode to Bo Peeps for breakfast. They make a lot of tasty skillet dishes, but I just got the potatoes and cheese. It's what the skillet dishes are all based on, but I've been eating too much and it seemed like plenty of food to me. On the way back, Phil and I detoured to ride on some of the local bike trails.

Later in the day, the Reelights we had ordered arrived. I installed them on my bike first and will install them on Phil's bike today, as his birthday present. While installing them on my bike, I discovered I had broken another spoke on the rear wheel. We called the nearby bicycle shop, but they said they couldn't squeeze me in. We called another place that also was nearby and they were too busy as well. I then called Bikeworks. The guy who runs the shop is a local legend that inspires strong feelings both pro and con. When he answered the phone, I explained I was from out of town and needed a spoke replaced. "What?" he said. "You're from out of town and you brought your bike with you? Well, bring it in!" He explained later that he was sure I was going to ask to rent a bike. He replaced the spoke while we waited and gave us lots of free advice along the way. I like the comment in the youtube comments that explains how you can't win: Try it yourself first, and you're an overconfident moron, but ask him questions without trying first and you're told to 'strap on a pair'." I was very happy to get my spoke replaced so that I can keep riding while I'm on my trip. Go Bruce!

Champaign

June 12, 2008 by Steven D. Brewer

Lucy and I left Kalamazoo today and drove to Champaign. We had a great time in Kalamazoo hanging out with everyone and going to the art fair. This morning, we started out early.

We drove to 5th street and, while crossing the train tracks, saw a box turtle. I rescued it from the tracks and put it somewhere safe. I hadn't seen a box turtle in years -- I don't think I've seen one in Massachusetts. He was a handsome, active fellow who'd lost a foot, but didn't seem the worse for it. I was glad to get him out of danger.

We met up with everyone, packed the car, and then saw Phil and Jackie onto the train. Afterwards, we went to what used to the Country Maid for a wedgie.

The place has changed owners and is now the Eldorado Cafe, but seems mostly the same inside. They still do a great trade. The wedgies seemed as good as they ever did.

Lucy and I hit the road before noon and decided to just take the expressway. Unfortunately, as we got close to Chicago, we saw a warning that I-57 was closed and suggested looking for an alternate route. We decided to turn south on highway 41 and then turned west on highway 30, which we hoped would be south of the problem. It was rather slow going. About half the way along highway 30, huge thunderclouds began to roll in and we had a driving rain storm -- a real toad-strangler. We crept along and eventually came out the other side, around the time we got to I-57. Unfortunately, it turned out that we were still north of the closure, so we had no sooner gotten on the highway when we were diverted onto a detour.

The detour went really slow. Looking at the map, we saw that when the detour went back west to meet up with 57, we could just continue south and 57 would eventually join us. We escaped from the detour and made better time after that. The road was in poor repair, however, and after several bone-jarring miles, we saw a sign that said "rough road ahead".

We arrived in plenty of time. We picked up beer and got pizza for everyone before Phil and Jackie got back and just sat in the shade drinking beer until they arrived. A satisfactory day. Tomorrow, we start trying to ride our bikes to Phil and Jackie's house.

On the Road

June 9, 2008 by Steven D. Brewer

Lucy and I took off on Thursday and began driving west. We took the Masspike and New York Thruway as far as Buffalo and then decided to head north, through Niagara Falls to take the Canadian route to Michigan. I've usually gone the other way to avoid the international crossings, but we'd brought our passports and had no problems crossing the border.

I've seen Niagara Falls before. I had kind of wanted to stop and see the falls again, but the parking lot close enough to walk to the falls charged $18. So, although we could see the falls from the car, we didn't stop and get out.

After that, we meandered around the backroads, trying to feel our way west to pick up the highway to Windsor. Eventually, we stopped at a little restaurant in Smithville for a country cooked dinner and then drove until after dark. We got one of the last rooms in Brantford and spent the night in a Days Inn.

This morning, we hit the road early, crossed back into the US around noon, and, stopping only for Fourth Meal, we drove straight to Kalamazoo.

We spent a charming afternoon and evening with everyone at Richard and Katy's house in the woods. A couple of large thunderstorms rumbled through and we sat in the screened in porch to listen to the rain and smell the fresh air. It was wonderful. Katy had prepared a delicious meal: salad, chicken with rosemary, fried potatoes, peas, and some good, hearty bread. After dinner, we had coffee and pie. We had great conversations about the kids and life and growing up and getting old.

Tonight, Lucy and I are staying in a Fairfield Inn. When we checked in, the guy mentioned that the storm had knocked out the alarm system and they were "working on it". What we didn't realize was that "working on it" meant manually setting off dozens of sensors and then then turning it off. And each time they set it off, it would sound an ear-spitting klaxon in our room. I'm a bit disappointed that the guy didn't mention we might want to go out for a drink for an hour or so until they were done. He claims they're done now and that it won't keep going off. If it goes off during the night, I'll be quite upset.

Tomorrow is the Art Festival in Kalamazoo. It will be nice to do something besides drive, for a change.

Organisms: Diversity and Interactions

June 7, 2008 by Steven D. Brewer

This fall, I've agreed to teach the online course I co-developed with Buzz Hoagland. It's an ecology course for practicing middle-school teachers working toward a Master's Degree in Science Education. Today, I met with Kathy Davis to talk about some of the new approaches I'm planning to try.

When I taught it previously, I was somewhat disappointed with the outcomes -- too many students would fade during the course and fail. Kathy has assured me that this was the result of students being subsidized and, now that students are paying their own way, they're more likely to be serious. (This isn't to say I didn't have serious students before -- some of the students were among the most dedicated I've ever had.)

One of the biggest challenges was getting student groups to function effectively. I'm hoping that using Organic Groups in Drupal will provide additional support for students working together closely. I'm also going to clarify the nature of the group work so that the nature of the interaction is more clearly circumscribed.

I'm also planning to add concept-mapping to the activities of the course. There is an excellent concept-mapping software package that allows group interaction and simulataneous editing of concept maps. The challenge is going to be reducing the other work required in the course to provide enough time for students to work on concept maps -- they're very time-consuming. Still, I think it may help make the conceptual structure of the course more concrete. We always knew what it was, but we worried that students sometimes came away with many of the conceptual relationships still vague.

Time

June 4, 2008 by Steven D. Brewer

Over the past couple of years, I got drawn into various leadership and governance activities. I got sucked into the vice-presidency of the Esperanto League for North America and of my local union (in addition to being the president of the regional Esperanto organization and chairing a couple of faculty senate committees, etc). The result has been that I've gotten stretched too thin. In July, I will rotate of the board of the MSP. When the "kandidatiga komitato had asked me about Esperanto-USA, I had originally agreed to continue to serve -- assuming no-one else wanted to do it. (When they had initially asked me, it was pretty clear they were scraping the bottom of the barrel). I was suprised when the ballot arrived and they had found someone to run against me! After being initially dismayed -- since they had clearly violated the spirit of my agreement to be a candidate -- I was relieved to know I wasn't going to have to do it anymore and I withdrew as a candidate. I'm free!

Esperanto-USA has serious problems. The main problem is that it doesn't really do anything. It's a placeholder for Esperanto activity in the US, but the real activity has largely routed around it by setting up the Esperanto Studies Foundation. ESF runs NASK (the summer Esperanto course) and is about the only thing that does any research or advocacy. Esperanto-USA does do some stuff. They have a membership (declining). They run a catalog bookstore. And there's a newsletter. It's an old-style social organization, like the kinds that have been dying out all over the country. Indeed all over the world. No-one really knows how organizations like these can survive.

It used to be that to participate in the Esperanto community, you needed to have some kind of guide or entr

Semester trails off

June 3, 2008 by Steven D. Brewer

The semester is trailing off into summer. I wasn't happy with how the semester ended up for my students. Some of them aren't happy either. I've felt bad for a few days -- wondering if there wasn't something more I could have done. But over the last couple of days, looking at the data and seeing to what lengths I went to rescue people, I've satisfied myself that I really couldn't have done much more.

I've replaced almost all of the computers in the BCRC. There is one left to go, but I've decided to replace that one with the workstation I had been using, so there will still be one PowerPC computer available for people who want to use the old Classic software, like PAUP. I've moved most of my stuff over, but want to check for another day or so.

On Thursday, Lucy and I start driving West. We're planning to visit Kalamazoo first, then head to Champaign for a few days. Lucy is going to stay in Champaign while I head on to BioQUEST.

I wanted to take my bike with me so we got a new bike rack for the cool car. We picked it up the morning and it works great. We should be able to take both our bikes and reduce the amount we have to drive around once we reach our destinations.

I also wanted to get Daniel his new bicycle before we left. His birthday isn't until early July, but seemed silly to wait to get him a new bicycle when he's really outgrown the one he's using. So we went to the store this afternoon and picked one out. We got him a mountain bike with cross-training tires. We were able to ride home from bike store (as is appropriate when you get a new bike) because I could carry my bike to the store on our new rack.

Daniel is very pleased. There is still plenty more he wants to get, however: a cyclometer, a light, toe-clips, and a camel-back hydration system to start. Tomorrow, we're planning to take a long ride and have a picnic lunch while we're out.

Faster

May 31, 2008 by Steven D. Brewer

I had originally intended to take a long ride today and made arrangements to be out of the office until 3:30 -- I needed to get away from the office for a bit anyway. But then it turned out that Charlie has a public science presentation at school about sustainability. So, instead of taking a long ride, I decided to try a faster ride.

The wind was out of the north, so I rode north into Sunderland. There is a long hill on the way into Sunderland, which blocks the wind to some extent and, since one isn't going all that fast anyway, the wind doesn't make as much of a difference. I remember this hill seeming more difficult in the past. On the other side of the hill, there's a long downhill run into Sunderland -- right into the teeth of the wind, but no problem since its downhill. In the middle of Sunderland, I turned left onto 47 and headed south. I took a quick break at the Millhouse Farm Market for a cup of coffee and started flying south. With the wind behind me, I could spin along at 15mph (which is pretty fast, for me). I love the way it's so quiet when I ride with the wind. Eventually, I turned back east to get home, but I rode around 13 miles at an average speed of more than 10mph -- I had been averaging less than 8 up until now.

Maybe I can fit in that long bike ride this weekend...

Short ride day

May 28, 2008 by Steven D. Brewer

Daniel kaj Lucy ?e restoracio After the long ride yesterday, I decided a short ride was in order today. Lucy, Daniel and I rode downtown to the Lord Jeff and had drinks and a light meal. I had a glass of chardonay and we shared an appetizer. It was another beautiful day and we had a wonderful time sitting in the shade and chatting in the warm breeze. The only downside was a nasty blower that the Lord Jeff has right by their exit that would run every so often, drowning out conversation.

I could have ridden quite a bit further, but this was perfect. It's all uphill to downtown, so after our brunch, we could practically just coast home. Tomorrow the weather looks like it will be unsettled. I'm hoping to get work taken care of before noon and have the rain finished up by then as well, letting me take a long bike ride in the afternoon. I think I'm about ready to circumnagivate the Connecticut River.

Long bike ride

May 26, 2008 by Steven D. Brewer

I took a long bike ride today, leaving around 10 and getting home around 2pm. I wasn't riding all the time -- I rode to the bridge along the bike trail and then explored the new extension into Northampton. I rode along King Street into the middle of Northampton and past to Northampton Bicycle. Then I rode back and turned right at the middle, went under the tracks and along past Joe's Spaghetti. I had a hankering for fried rice, but the Chinese places weren't open yet. So I rode back along the bike trail to Whole Foods and stopped there. I couldn't find fried rice, but I did see a weird "forbidden black rice salad" that looked cool, so I got some of that and some clam chowder. The last 5 miles were the toughest: its the endless hill part of the bike trail and then there are two small climbs at the end of the bikeway connector and by Computer Science. It looks like I rode around 25 miles, all in all. It was about the right amount for the day.

The bike trail is one of the best things about the Amherst area -- it gets a lot of use. There is work going on near the bridge to smooth out the places where roots have created rough patches along the trail. Some places are so rough that you can barely ride, but there are only a few places like that. It's a very restful way to ride a bike, without having cars zipping by just waiting to clip you.

Afterwards, I had planned on going to my office to finish off grades, but the weather is just too nice. It's sunny and cool with a very light breeze -- simply perfect weather. Maybe it will rain tomorrow and make it easy for me to sneak into the office for a couple of hours. But not today.

My class is like a bog...

May 25, 2008 by Steven D. Brewer

Chatting with Phil this morning, I realized that my class is like the boardwalk at a bog. A handful of students just stand at the trail head and never walk out onto the boardwalk at all. A fair number of students just tramp on through. They start on one side and walk straight through to the other side, staring straight ahead the whole time. Some pay so little attention to where they're going, they miss a turn, fall off, and get sucked down into the mud. Others look around and discover cotton grass gently waving in the breeze, beautiful delicate orchids, interesting carnivorous plants, fascinating biological diversity, and compelling natural beauty -- they have a great time and some tell me it was their favorite experience at the university. All the while, I wave my arms and try to get people to look at the cool stuff or run around trying to pull people out of the mud. As the mud closes over them they say things like, "Why did you make us walk on this boardwalk anyway? Why couldn't we just drive around the bog on the highway?"

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