Bierfaristo Blog

My life has many threads. I had to come home today because the contractor repairing our house after trees fell on it (back in May) needed to get in to do some drywall work. Finally, the main work is done: the roof over the shed dormer is replaced and the work to bring the structure of the roof up to code is completed, and all the siding is back on the house. While we had the roof open, we got a lot more insulation installed too. Now, there are only a half-dozen small things to finish up.

While I was home, I found that there had been a power outtage in the building long enough to take down most of the department servers. And when they came back up, there was a problem with network connectivity in the intro labs. Or maybe it was authentication. I could talk to the machines via ssh, but couldn't authenticate. We've finally gotten ldap working -- after years of trying to make it happen and months of work. But now it wasn't. But it was working some places: the web authentication was working. And it was working in the other building. With those pieces of data, I realized that there must be a problem with the iptables on the NAT gateway so that ldap connections from clients in our building were being blocked. Sure enough, I found that the script that sets up the ruleset was not the most recent one. I flushed the rules and ran the correct script and stuff started working.

Other threads: Tom Hoogendyk and I have set up a system for managing digital signs in the building with a recipe based on drupal. The system has generated excitement at the college level where the experience using proprietary systems has been poor.

I've been trying to put the pieces in place to take a sabbatical working on an interesting project with the people at Sandy Point. Trying to get the University and the funding and the project all lined up has taken a lot of time recently.

I also had to fill out my AFR and go back over the past year and reflect on what I've accomplished -- and how little I've been able to focus on Science Education. I'm hopeful that we can find a way to rebalance my position so that I get to spend more time building educational resources and less time just managing infrastructure. You need the infrastructure to build the resources, but it's not what gets me up in the morning.

The haibun I wrote has been accepted at Belletra Almanako. It's about a father-and-son outing to Mount Sugarloaf. I'm working on the next haibun, about a Columbus-day road-trip a couple of years ago. And i have another story I'm thinking about submitted to Literatura Foiro. I've also been having fun writing some fiction. I had an idea for a story and have been exploring whether to try to make it into a novel. I started writing it before NaNoWriMo and, although I have an idea for another novel I'd like to write -- and I'd really like to participate in NaNoWriMo, I decided I couldn't spend the time.

Too many threads.

I recently read two interesting articles about atheism. The Globe has a bit about Daniel Dennett who found that members of the clergy don't necessarily believe what they're preaching. I had wondered about that.

That’s the joke that we often provoke from people when we talk about this: Anybody who goes through seminary and comes out believing in God hasn’t been paying attention.

The other article was in the Opinionator at the NYTimes and was about the supposed challenge of having morals without God. He says

While I do consider religious institutions and their representatives — popes, bishops, mega-preachers, ayatollahs, and rabbis — fair game for criticism, what good could come from insulting individuals who find value in religion? And more pertinently, what alternative does science have to offer? Science is not in the business of spelling out the meaning of life and even less in telling us how to live our lives. We, scientists, are good at finding out why things are the way they are, or how things work, and I do believe that biology can help us understand what kind of animals we are and why our morality looks the way it does. But to go from there to offering moral guidance seems a stretch.

Even the staunchest atheist growing up in Western society cannot avoid having absorbed the basic tenets of Christian morality. Our societies are steeped in it: everything we have accomplished over the centuries, even science, developed either hand in hand with or in opposition to religion, but never separately. It is impossible to know what morality would look like without religion. It would require a visit to a human culture that is not now and never was religious. That such cultures do not exist should give us pause.

Really? This argument seems entirely specious to me: maybe the reason that such cultures do not exist is that the religious cultures have killed them off. I agree that we don't know what morality looks like without religion -- but we can see what it looks like with religion. It looks like crusades and inquisitions. What might it look like without the millstone of religion dragging it down. That's what I'd like to know.

Lucy and I had a nice time at ARE again this year. Beautiful weather and good autumnal color.

During the first evening, we had the "amikeca vespero" where we played meet-and-greet games to get to know one another and then went out to a bonfire to tell stories in the dark.

I wore my black trenchcoat and top hat, which generated commentary from many people. One woman asked "Who are you?"

"Doktoro Brewer," I replied.

Then she asked "Who's that?" to which I replied by handing her my business card. It was as succinct an answer as any I could make.

The Department had its annual retreat yesterday and, I thought, showed more coherence than in past years. I think it speaks volumes about the leadership of our current chair, who has worked diligently at building effective structures for governance in the department, stimulated much greater interaction among the faculty, and has been tough when necessary. The result is that the retreat felt like part of an on-going discussion.

We had an extended discussion about the curriculum. We made plans to start a regular discussion group around teaching and learning. We looked at data from the senior survey and discussed how we could improve the student experience. I believe that one of our challenges has been that a significant number of students become a Biology major merely because the name is familiar -- not because they've considered their choice carefully and selected the best department for their interests. This has several effects: one is that we have a large population of majors and another is that a significant portion is compose of students who aren't making critical choices. These students reach the end of their studies and discover that their degree (absent any conscious effort on their part) doesn't prepare them for any particular career track. One thing we clearly need to do better is to provide more guidance to students so that they do use their time at the University to prepare more effectively for their life afterwards. But more effective mechanisms for helping students choose Biology affirmatively (and considering other departments critically), might help us as well.

We also discussed a variety of other topics: supporting the research mission more effectively and adjusting the name of the department. The discussion was spirited, but consistently respectful and with a sense of shared community.

Today, I again spent the whole day putting out fires. And the problems all have cascades and interactions: I needed to move the histology site to the server in the ISB and, as I was doing the work, I was reminded that the default paths on the ISB server are still broken. And I found that the version of drupal there wasn't up-to-date, so I updated it. And the update overwrote .htaccess and broke the password changing stuff. And while I was looking through log files, I found that people had links to bad, outdated URLs for password changing, so I put in redirects. And that's the simple, streamlined version of just 5% of what happened today.

While I was in the middle of stuff, Alisa called, angry with the contractor. They didn't come on Monday, like they said they would, and they wanted to ask her a question just as she was leaving, and this and that and the other thing. When I finally hung up the phone, it was all just too much. I got up and walked down to the courtyard, and sat there for 20 minutes just looking at the sky and the flowers and listening to the wind.

Alisa called back and said that things were OK. I took at deep breath and went back to my office. But I fixed myself a little lunch, took a little time for myself, and then threw myself back into things and got, at least, most of the stuff that had gotten unwound, stuffed back into place.

It's been the busiest, craziest, toughest beginning of the fall yet. Something really has to give.

I watch the BBC most nights, which has been offering rapt coverage of the Pope's visit to Britain. They've described his goals in speaking as the "re-evangelization of the West". I was interested to see what he was actually saying, so I googled looking for a transcript. The one that showed up highest (that wasn't something old about John Paul) was a post at the Richard Dawkins Foundation. There's something ironic in that -- more about that later.

Oversimplifying a bit, Benedict argues that the good parts of British tradition (justice, truth, mercy, etc) are the result of their religious heritage. He believes that most of the tragedies of the 20th century were the result of "atheist extremism". And he concludes that the exclusion of religion results in a "truncated vision of man" and his destiny. I believe all three things are false.

I believe that religion is far more dangerous, by dividing people based on their metaphysical beliefs, beliefs that can have no grounding in reality. Clinging to ancient mythology as the basis for truth, justice and the foundation for a path forward is a recipe for disaster: it's like building on quicksand. Our only hope is to build a common foundation together among things we can all agree upon and not cling to dangerous fantasies that can be used to divide us.

In the end, however, I was not surprised to see the transcript at RichardDawkins.net. One of our great challenges is that relatively few people actually read the words of the people they follow or that they despise. How many people will actually read the Pope's words? How many people have actually read Osama bin Laden's proclamations? How many people have actually read Barack Obama's economic plan? These days, most people seem to wait for the media to tell them what to think.

Rodger is using computers in the intro labs to run a giant phylogenetic analysis for his dissertation. He was planning to walk around with a flash drive to run the analyses, but I persuaded him to let me build some resources to do it over the network. For a long time, I've wanted to have a mechanism that would facilitate people distributing jobs out to all the workstations in our computer labs. We built the first part on Friday.

I started by looking at Apple's "Folder Actions" -- I thought maybe we could just create a folder that we could put stuff in and have an analysis run. But it turns out the Folder Actions are bound to a particular user and only work when that user is logged in. Fail. The mechanism that makes them work is also spread out all over the freaking file system: parts in ~/Library/Preferences and in /private/var/db/ and uses an undocumented faceless binary that is located in some hidden folder someplace. Ugh. So much of what Apple does looks shiny on the outside, but is implemented in a way that's seriously difficult to build on.

After wasting an hour building an Applescript that would implement a folder action, I started over and made a launchd file that would start a PHP script to run the analysis. It works great: it grabs a file, makes a directory with the same name (minus the extension), puts the file inside, and launches Beast. And same strategy could be used to launch any other kind of analysis or process.

We ran into a few bugs getting the whole thing working: first, we found that Beast wasn't getting launched with enough memory, so we had to modify the flags it was getting launched with. Then we had to get it out to all the machines in the intro labs, and we found a few machines that hadn't gotten updated properly and had to fix those. Then we ran into a really baffling problem: we could only ssh into one of the four intro labs.

At first, when Rodger reported it, I didn't believe that the problem was happening. Then I tried it and found that it was in fact true: I could ssh into the one new lab, but not into the other three older labs. I alerted the technical staff and George and I walked through everything: Yes, the machines were configured properly. Yes, you could ssh into them from themselves. Yes, you could ssh into them from other servers. We narrowed down the problem to just the one server: it could ssh into one lab but not the others. We looked at the arp tables, checked the netmask, nothing. At the end of the day, we rebooted the server, but the problem persisted. Then George suggested checking the name resolution. "Right! Maybe it's the hosts file," I said. "It doesn't have a hosts file," George said. "Oh, yes it does," I said. And, in fact, the hosts file was ancient and had bogus entries for the intro lab machines that weren't working. Once we cleaned those out, it worked fine. Whew.

The next step in the system is to set up shared-key authentication for moving the files and an automated system to put the files across, poll for completion of the job, and then pull the results back. But even with that, it's still a lot more convenient than walking around with a flash drive.

The first day of classes went quite well. I put out various small fires that arose, then prepared for and met my class of writing students. The class flew by all too quickly as it does, but I believe that I hit all the things I wanted to be sure to touch on in class. The students seemed enthusiastic and I'm looking forward to a good semester.

On Sunday, there was an article the Globe that put a spotlight on UMass. The summary was "Hampered by years of cuts, Amherst campus struggles to draw ranking Bay State students" and the focus was on Massachusetts students going out of state to find public higher education. The article resonated with me at several levels and I though it really hit the mark in several places.

UMass’s challenges, though, run deeper than its reputation problem among many prospective students. It is a campus in crisis, professors say.

The Amherst campus has lost nearly a fifth of its tenure-track faculty over the past two decades as a result of the state’s financial woes, leaving only 972 permanent faculty on a campus of 20,000 undergraduates. In comparison, the 17,000-student UConn employs 1,286 tenure-track professors.

UMass’s English department, once 100 strong, has dwindled to 43 professors.

“It’s been difficult, very difficult,’’ said Joseph Bartolomeo, the English department chairman. “We struggle to get back to an earlier level and then there’s another cut. That is very demoralizing for the faculty.’’

You could say the same thing about Biology. When it was formed, we had around 60 tenure-system faculty. Now there are 26.

And then there was this:

“Instead of just saying, ‘You have a $6,000 scholarship as part of your financial aid package,’ we said, ‘Congratulations! You’ve been awarded a Chancellor’s Scholarship for $6,000, and you get a certificate to hang on your wall,’ ’’ he said. “That’s kind of a marketing tool.’’

The chancellor sent a broadcast email to the faculty expressing his outrage over what he perceived as a negative bias in the article.

But what's happening here, is happening everywhere else too. Bob Samuels wrote a somewhat naive post about unionizing non-tenure-system faculty. I say naive only because a number of faculty unions have been organizing non-tenure-system faculty aggressively for several years. Similarly, the Chronicle had an article about the death of the humanities.

At the bottom is a shift in the United States away from the idea of a common good. Over the past forty years, the US has shifted from a belief that we can build a future together to one where everyone is a rugged individualist that needs to earn their own way. And, whereas we used to require those who had benefited most to pay a larger share (ie, higher incomes were taxed at higher rates), now the largest burden has been shifted onto the poor and middle class. And so, while GDP has continued to go up over the past 40 years, wages -- and tax returns -- have been stagnant. As state support for higher education has declined, Universities have increased tuition. And as state support for financial aid has declined, UMass has started self-funding a lot of the financial aid. This particularly hurts the middle class that makes too much money to receive financial aid, but increasingly is paying the burden for everyone.

Today, I spent a few hours and got things ready for the start of the semester. On Friday, I was so busy -- and got interrupted so many times -- that I just couldn't get things finished. There was no-one in the ISB today, so I finished the image for the Molecular Evolution course (they needed a handful of command-line programs installed) and, while that was updating, I got my writing course website mostly set up. I still have to set up the intro labs, but labs don't start until next week, so I still have a few days.

I've been spending a lot of time thinking about the "theme" for this semester's writing class. I've generally tried to look for something to drive a data collection exercise. Last semester, we did a "calling frog" survey. Another semester, we mapped the location of garlic mustard plants in Amherst. The problem is that, in the fall, the conditions are not favorable for doing field studies -- and I don't have a laboratory for the course. (In point of fact, next semester, I'm planning to try to schedule my course in the ISB, so I'll have a lab. But this semester, I'm still on the hook...) One year, I had my students study cockroaches: I thought that was perfect. We could find cockroaches in the building and study them. I thought the students would be ecstatic to be studying animals. But, for some reason, the students didn't enjoy studying cockroaches. Go figure.

This semester, I'm thinking I'll have the students construct computer models and study those. It would free us from having to go outside in the snow. And it would make it easy to get lots of cool data. The question is now, what to model. But we've got a whole semester to figure that out.

The other day, I decided to try installing the twitter_pull module and found that I was a full major revision out-of-date with my blogging software. So, over the long weekend, I spent a couple of hours updating and retheming my blog. I decided to use the Newswire theme, which I've been using at E-USA for a year or so. It's a really solid theme. I rejiggered stuff a bit. It's not perfect, but it's probably close enough.