Writing in Biology: Choosing a theme

Before I started posting about what I do each week in Writing in Biology, I should probably have drafted a post about establishing a "theme" for each semester. The theme ends up affecting many of the exercises I have students do and some of the scheduling of events.

By "theme", I mean a topic or subject area that the course is going to focus on for the semester. This often will affect what organism/object I choose for the first "writing from experience" exercise, what papers I choose for students to look at in week 2, and will limit the scope of what kinds of research proposals and projects we'll work on.

I've tried teaching the class both with and without an organizing theme. My sense has been that it works better to have a theme. A theme usually gives students ideas about the kinds of things they might do. Having no theme leaves students adrift trying to come up with ideas. Students also frequently want to choose inappropriate topics for research (human subjects or vertebrate research that would require complex paperwork to conduct) and choosing a broad theme that excludes those topics, takes them right off the table.

I usually try to pick something that I don't know much about. I do this, in part, because it's an opportunity for me to learn stuff. But also because I'm much less likely to become overly directive if I don't know too much about it. When I've picked a topic I already know pretty well, I find that my opinions end up guiding students too much: they're better off to go into the subject themselves.

Some of the themes worked pretty well. I was particularly pleased with the outcomes of studying vernal pools, tardigrades, garlic mustard, and planarians. Successful themes seem to incorporate a mix of student wonder and importance.

Less successful themes were not disastrous, but didn't pique students' interests for whatever reason. I'm reminded of the semester we studied cockroaches. I picked the theme because I was aware students generally prefer to study animals to plants, but finding an animal to study in November/December is challenging. I thought that we could catch cockroaches in the building and look at demographics/diversity of the populations. But students seemed to regard cockroaches not as "animals" but as mere "vermin" unworthy of study.

One challenge with teaching for participation is that each group of students is different. And even just one or two enthusiastic -- or recalcitrant -- individuals can make a huge difference in the atmosphere of the class. In one semester, I coordinated with the Amherst Tree Warden with the goal of having the data we collected be also a community service learning project with the Town. But I had a student who was seemingly a devotee of Ayn Rand and complained bitterly for weeks about being "forced" to do "free work" for the Town.

In point of fact, when it comes to writing a proposal or project, I don't let the theme interfere with a student, or group, that wants to write about something else. It is always my goal that students who really want to write about any particular thing should be supported in their aspirations. The whole point of my teaching is to liberate students to use the class to pursue their own interests, after all.

Writing in Biology: Second Class

I start off every class by checking in with students to gauge the temperature of how things are going: Any questions? Where are we? What are we doing today? In the first couple of classes, I tend to be more directive with the goal of reassuring students that the class is not some weird, untraditional experience which can rattle some students: In each class, I try to drop the reins of control and give students their head to use the course for their own learning.

In most weeks, I take a few minutes to point out the readings I had asked them to do and encourage them to use the book and other readings as they're doing their writing. I take a few minutes to make a case that this week's reading about paragraphs is particularly important -- for writing the weekly perfect paragraphs and commenting on other people's paragraphs. And to point out that all of their writing should result in carefully focused paragraphs with (referring to the textbook) a topic sentence, consistent order & point of view, cohesive sentences, key terms for continuity, and transitions.

I've also asked them to read "The One Right Way to Talk Science" in Lemke's Talking Science. This chapter, which is actually about avoiding the mystique of science, has an excellent list of characteristics that a writer can deploy to emulate scientific prose. I organize these, with some examples as an introduction to "Uncreative Writing":

1. Be as verbally explicit and universal as possible.
2. Avoid colloquial forms of language.
3. Use technical terms in place of colloquial synonyms.
4. Avoid personification and use of specifically or usually human attributes or qualities.
5. Avoid metaphoric and figurative language.
7. Avoid personalities and reference to individual human beings.
8. Avoid reference to fiction or fantasy.
9. Use causal forms of explanation and avoid narrative and dramatic accounts.

For class, I've provided two bibliographic references that I've asked them to find and skim -- mainly to check that they can find a bibliographic reference with recommendations on how to use the library's proxy service to get access to publications from off-campus. One paper is a review paper and the other is a research paper. My goal is for them to recognize that one has content-based headings and the other has the traditional headings of a research paper. Many of the students have never been aware of the existence of two kinds of scientific articles and it's always interesting to ask them what the authors of the review paper "did". My main point is to draw attention to the structure of a research article: how each section plays a particular role in the manuscript. And how the form is highly synthetic and artificial.

Having been talking for a few minutes, I ask them to do an activity in pairs where I provide each pair a link and ask them to evaluate the linked webpage/site to comments on its reliability and trustworthiness. I provide links to a range of sites including Google, Google Scholar, Wikipedia, Encyclopedia Britannica, Science, Trends in Ecology and Evolution, a predatory journal, news sites, a click-bait propaganda site, think tanks, non-profits, and some parody sites (like the Tree Octopus page). We explore their thinking and then use the CRAAP test as a tool for evaluating reliability.

I then provide an overview of the METHODS project pointing out the goals and various steps and checkpoints along the way. As they're about to start writing a methods section, I have them do a "narrative to exposition" activity I've developed. I ask them create a fine-grained list of all of the (public) activities they did on a recent day, e.g "I woke up. I got up. I put on my glasses. I walked downstairs. I made coffee. I checked my email." After they have the list, I ask them to organize all of the activities into categories. Then I ask them to write a paragraph that explains what each category is and summarizes all of the instances of those activities. The goal is to transform their methods from a story, organized by time, to exposition, organized by the accomplishment of goals, irrespective of order or time. I point out that if they are tempted to use the word "then" in writing their methods, they're probably slipping into narrative rather than exposition.

As the last activity of the day, I show them a picture I've found that is deceptive in terms of scale. It shows an Alfi wood-fired hot-tub, but without any other objects for scale. Most people seem to think it's something for the kitchen, and are astonished when a picture showing a woman bathing reveals its true scale. I use this to point out that pictures they take for their methods projects should include some object for scale, so you can know how big something is: I recommend printing out a page of paper rulers and using one of them, although pointing out that other objects can work as well, e.g. coins.

We end by looking at the prep page for the following week where I've asked them to look through some scientific articles to find a multi-panel scientific figure that is good or has particular qualities they like. And to bring the imagery required for their multi-panel figure, with the goal of working on their figure in class.

Repeating History at the MTA Annual Meeting

It's always interesting to attend the MTA Annual Meeting. It's a perfect example of watching people who don't know the history undertaking to repeat it. Every year. I wonder if anyone has written a history of Annual Meeting. I'm skeptical that you could get people to read it, but we are talking about teachers: they might.

There are two truisms about annual meeting: (1) everyone has an opinion and (2) people quickly get tired of hearing other people's opinions. Trying to strike a balance between letting people talk and trying to move ahead with the business of the organization is an endless challenge. Every year, people try to tinker with the standing rules trying to adjust this balance. This year was the same.

For this to make any sense to anyone who hasn't attended Annual Meeting, a quick precis is probably necessary. Annual Meeting is conducted in a giant hall with 1000-2000 people seating in blocks by "region". In the front of the hall is a platform with a long table and a podium and three giant screens. There are 8 microphones and cameras set up among the participants. At each microphone is a box with large colored signs you can hold up. You hold up a different color to be recognized for different purposes: a yellow card, to ask a question; a green card, to speak in favor of a motion; and a red card, to speak against a motion. The standing rules define exactly when you can make a motion and what kinds of motions you can make with each color and which takes precedence. There is a parliamentarian and several staff members who scan the audience and pass cards to the president with which microphone is next in the speaking order.

Normally (I use this term advisedly), the maker of a motion can speak to a motion (on a green) and then the floor is opened to questions (yellow cards), and then people can debate the motion using green and red cards, but questions can still take precedence. Once all the questions have been answered and everyone has spoken, there is a vote on the question and the motion is adopted or rejected. As I say, "normally." But normally has nothing to do with it.

In point of fact, teachers are gifted at rhetoric and love to fill time with the sounds of their own voices. They love the challenge of using a "question" to actually speak for or against the motion. Or trying to block "the other side" by asking question after question to thwart debate. At the same time, the body, as a whole, tends to lose patience with people trying to gum up the works. These tactics lead people to make motions to "close debate". But you can only make a motion to close debate on a red or green card. And when there's a sea of yellow cards, red and green never get called. So they changed the standing rules a few years ago to allow you make a motion to "suspend the rules" (which requires a 2/3 vote) on a yellow card to change the order of precedence to allow green and red cards to be called. But often this happens after people are already so frustrated that someone will call the question and end debate before any actual debate has occurred.

OK. So this year, someone had the clever idea of requiring two green and two red cards before someone could make a motion to close debate. After much debate (and tempers already wearing thin), this change to the standing rules was adopted. And lasted for about two motions. Pretty quickly, people from the opposing side started holding up green cards and then not actually speaking in support of the motion, purely to thwart the rule. I called a point of order to ask whether these sham statements of support "counted" and was told that they did because to do otherwise would require the parliamentarian to ascribe intent. Shortly afterward, someone moved to suspend the rules to undo the new change in the standing rules.

This turned out to be convenient because the next day, as the temper of the body grew even shorter, we were anticipating that a group would try to offer amendments to tinker with the budget. So while the questions were still being asked, I stood with a green card and my colleague Dave took a red card and we waited (and waited and waited) until we could make a motion: and so I was first in the calling order and called to close debate. They tried to make a quorum call, which failed. And then my motion, and the budget, passed easily. Yay me.

What I'm not talking about, of course, are the underlying dynamics and tensions. I'll leave those for another post.

Testimony for Cherish Act hearing

I drafted comments to be presented at the Cherish Act hearing tomorrow at the State House.

Biology is a discipline where modern facilities and equipment are critical to providing an effective education to our students: to prepare them to move seamlessly into the growing life-science industry. Unfortunately, after years of declining funding, our introductory biology facilities had suffered.

We have been successful at attracting large grants from Howard Hughes Medical Institute and others to make improvements over the years, but those organizations are rarely interested in funding the basic infrastructure.

Recently, the University re-introduced "lab fees" to raise money from our students and their families to fund these needed renovations. This purchased new lab benches and facilities for more modern labs. But it's yet another example of the state shirking its responsibility to provide for the basic needs of the curriculum and requiring students to shoulder a larger burden, through debt, that many will still be paying for years to come. It's disgraceful and makes me ashamed to be a part of the institution.

Exactly the same is true regarding the new "technology fee." The University should be funded sufficiently to provide the basic infrastructure needed for a 21st century education. Students should not be going into debt for our necessary facilities and infrastructure.

Please fund our future and pass the Cherish Act.

I am hopeful that, after years of declining state funding for public higher education (we're still below 2001 funding levels) there is enough momentum to pass this act which would bring funding up to 2001 levels over 5 years during which time we could freeze tuition and fees. We can always hope.

Melamine Effect

In the book Punished by Rewards, Alfie Kohn describes the perverse effects of incentive systems. Incentive systems fail because it's always easier (and cheaper) to game the system than to actually win. If you incentivize "call length" in a call center, for example, employees will hang up on people. If you incentive "resolutions" the staff will find short cuts to mark calls as "resolved" rather than to actually solve people's problems. He found that the best way to get people to do good work is to compensate them adequately and support their efforts to do good work.

Several years ago I wrote a post about educational measurement in which I described a phenomenon I have come to call the Melamine Effect. In 2007 and 2008, pet food and then milk were found that were contaminated with melamine. The consequences were horrific. In 2007 hundreds of pets were killed. In 2008, tens of thousands of infants were poisoned, many suffering liver damage. Several died. It turned out that unscrupulous people were diluting milk with water and then adding this cheap, industrial chemical — that coincidentally increases the score on a widely-used test for protein content — as a way to increase their profits.

Seeing the effects that standardized testing and so-called education reform were having on schools, I realized that the circumstances are perfectly analogous. If you measure something and use that measure to understand natural systems, you're fine. But if you start looking for treatments that will shift the measure, you're inviting all kinds of perverse effects, because educational measures can't actually measure what people are interested in (i.e. learning or understanding): they only measure factors that tend to covary with them in natural populations. Once you start applying treatments -- especially the cheapest ones -- you're almost assured of toxic effects.

And it should go without saying that just changing a measure doesn't mean you will actually produce better outcomes either. For years, people were told to take niacin to improve their cholesterol test scores. But a long-term study revealed that, although it did improve the scores, those gains were not actually associated with reduced risk of disease.

For a while the term was "data driven", but more recently the term is "evidence based". When people start using words like this, your hackles should rise. Look critically at the underlying model and how it relates evidence to the dimension of interest. This isn't always easy with the "dashboards" of the modern analytics systems. But it's the only way to avoid the "melamine effect".

Writing in Biology: First Class

Before the first class meeting of Writing in Biology, while the students are coming into the room before class, I invite the students to play a parlor game. I usually show up about 10 minutes ahead of time and, as the students trickle in, I invite them to play Anne Miller from Cripple Creek. In this game, you guess what things Anne Miller likes and doesn't like, usually presented as pairs of things that she likes and doesn't like that, on the surface seem similar or contradictory. For example, Anne Miller likes "glass", but doesn't like "windows". I explain that the same is like science: you need to construct a hypothesis and then test the hypothesis. Once everyone has arrived, we begin the class.

I start out trying to provide students with a reasonably familiar classroom experience. In the long run, I'll want to draw myself out of the center of the class. But I've found that if I start out that way, some students are very uncomfortable, so in the first class, I'm pretty directive -- more than I would ideally want to be.

I introduce myself. I speak briefly about my education and history at the university. I tell them my pronouns, where my office is, when my office hours are, etc. And I tell them that they "have me" for the semester: if they have any questions, they are invited to stop by my office anytime (or make an appointment if they want to be sure I'm there.) And that they're welcome to call on me, not just for questions about the class, but anything else at the University. They're my students and although I might not be able to fix everything, I'm happy to help them figure out who can -- and to help them follow up if something isn't working.

At this point, I ask them to move their chairs into a circle (leaving them in rows to start, is part of the "familiar classroom experience"). And then I have them introduce themselves to the people sitting nearby. I explain that then I'll want each person in the class to be introduced to me by someone else who should tell me their name and the answer to a question. I usually use "what kind of tree would you want to be and where would you grow?" I've occasionally picked other questions, but the tree question works pretty well as a quirky icebreaker. After a few minutes, I start going around the room and have each student introduced to me and begin rehearsing the names in order out loud. "Bob, Karen, George, etc. etc." It turns out it's trivial to memorize 25 names more-or-less in order. I had a professor who could do it with first and last names of 60 students and required everyone in the class to do it as well (each student had to introduce all of the previous students.) I don't do that because it's stressful for the students. Once I get to the end, I usually get a round of applause from the students and I joke that they must always sit in that order from now on. It turns out that many of the students tell me that have never been in a class where a professor learned their names. Which is sad. I promise them that I will do my best to learn everyone's names and they should help me remember.

The key exercise of the day is an observation activity. I give each student an object for them to observe and write about. The object I select varies depending on season and availability. One year, I gave each student a live baby scorpion to observe. In the semester we studied spiders, I gave each student a live Cellar spider (Pholcus). I've often used meal worms (sometimes two different kinds, without telling them that they're not all the same.) Bait shops often have interesting little maggots (spikes) and caterpillars (waxworms) which are good. My favorite are Eristalis larvae called "mousies" in the bait trade. The goal is to have something living and unfamiliar. If something is too familiar (like walnuts), students won't bother to look carefully.

Before class, in the first week's prep page, I have asked them to read Chapter 7 of Louis Agassiz as a Teacher before class. In that story, Agassiz has a student observe a fish for days and write observations. I invite the students to sit for two sessions of 15 minutes to observe and write down everything they notice: To start with just a list of ideas, then to identify questions, and to try to turn the writing into paragraphs. In 15 minutes, we share some observations and reflect a bit on what they've been able to observe and the kinds of tools that might help observation. I've usually printed off some paper rulers that I pass out and encourage them to think quantitatively. After another 15 minutes, we through other observations and then I ask them to count up how many words they wrote in a half hour.

At this point, I go through the structure of the class: I briefly touch on my expectation for weekly draft writing (3 hours divided into 30 minute chunks that they work into their schedule). If they ask how many words they should write, I point out that they just counted how many words they could write in a half hour and that if that was how many word they could write about a maggot, they should surely be able to write about something really interesting. I explain the Perfect Paragraph activity, and describe each of the major projects in turn (Methods, Research Proposals, Research Projects, and Reflective Essay.)

We take a break for a few minutes at this point and reconvene in the Biology Computer Resource Center. I make sure they've set a password for their Biology Account and ask them to confirm they can log into our computers and ask them to log into the Biology Department website I use (which I will describe separately). We spend the rest of the period making sure they can log in, create a blog post as a draft (with some of their observations), create a second post as a Perfect Paragraph, and then comment on someone's Perfect Paragraph.

At the end of class, I point out the prep page for the next week, briefly describe what it contains, when prep-pages will be posted, and ask them if they have any questions.

And that's the first class meeting.

Writing in Biology Retrospective

I first started teaching Writing in Biology in 2002 when several senior faculty retired and the Department was having difficulty finding new instructors to cycle in. In Biology, the course was considered a "short straw" assignment and was taught by a mix of tenure-system and non-tenure-system faculty. I saw potential to have students do projects and write about them and volunteered for the assignment.

Every major at the University is required to offer a junior-year course on Writing in that discipline. The Faculty Senate approved the plan in 1982.

Each department, school or college, in consultation with writing specialists, will determine what kinds of writing competence its majors need.

I don't know if this ever happened in Biology. Two of the retiring faculty gave me their course materials. In consultation with materials from the Writing Program, I developed a version of the class and began teaching it. The course has evolved in small ways since then, but structurally is still largely the same as when I first taught it.

In part, I used the course as a testbed for new technologies: I used wikis early on, then migrated to Drupal with revisions, and most recently have used Google Docs. I even put up an instance of Moodle and used that for one semester, long before the campus adopted Moodle as a learning-management system.

At first, the deliverable for the final project was a manuscript, like the others. But after the chair balked at purchasing a poster printer in response to a new faculty member who wanted one, I made a persuasive pitch that my volunteering to teach the class freed up sufficient funds to justify the purchase so I could use it to have students print posters.

When they shortened the semester by a week, I dropped one of the projects. I used to have students to do a mini "observation project" during the first two weeks of the semester. I really liked the project as it provided a microcosm of what completing one the projects took.

Over the years, I've added a variety of in-class and pre-class activities primarily in response to recognizing specific deficits that students tend to come into the course with: transforming narrative to exposition, writing figure legends, etc.

Over the next few weeks, I plan to write a series off posts to describe the goals of the class and how I try to create an environment for students to achieve those goals.

BCRC Server Update

We updated the BCRC server over spring break. We've known we needed to do it for a long time now, but have been putting it off because we have old Drupal 6 sites that need to be migrated, I've believed that they (or some of their modules) will probably not work with newer version of PHP in this version of Ubuntu. During the Fall, we updated the server in the ISB and, to prepare, we tested and I rewrote some of the old legacy code that I had written. So we knew that much. But this server was enormously more complicated.

It turned out there were only two serious problems with my old code. Originally, PHP used its own regular expressions library (ereg) but, at some point, started including functions against the perl regular-expressions library (preg). I've probably been using PHP since before it had either. But I had to make minor API changes and update my functions to use perl regular-expressions. I also had start using mysql very early and those functions had become deprecated, so I needed to make minor changes to all of those.

The first serious problem was that our MySQL databases didn't get updated properly. The updater is supposed to be able to ask mysql to update the databases, but something went wrong. At first, mysql wouldn't start at all, I think because it was confused about which my.cnf it should be reading. This was probably why the update didn't work correctly. This server has existed since ~1995 and was originally a Sparc 10. Then we got an E250, then a T5220, and most recently a Supermicro running Ubuntu. But a lot -- too much -- of that history is still there. Once I cleaned up the my.cnf files, we got mysql running, but it couldn't read the database of users and so nothing could get access to its data. It turns out that to update the database, you need to log in as "root" so if you can't log in, you can update the database. So then I shut down the service and started it manually with --skip-grant-tables. Then I was able to run the upgrade script. Then mysql came up. (Note this story actually skips several epicycles I made trying to sort out the problems, but is what I did in the end.)

Before the migration, I had started re-building a new web-tree around Drupal 8 (rather the old tree which was built around Drupal 6) hosted at a different CNAME. I had migrated the key pieces of what I wanted going forward, without taking down the old web-tree. After the update, I switched to the new web-tree and then migrate stuff out of the old tree to the new one. I figured this was potentially more disruptive, but safer: there was a lot of old history that was infested with bitrot. It seemed better to start with known good things and then rescue stuff that people identified as missing after-the-fact.

There are still a lot of rough edges: broken paths, missing images, stuff that needs to be reconfigured. But basically good to go. The two most complicated updates are yet to come. But this was a good test-bed to help us prepare for what we need to do for those.

How to Reduce Cheating Without Evil Robots

Recently, Turnitin was purchased for $1.75 billion dollars. Turnitin is the malicious corporation that neoliberal universities use to de-skill faculty labor. Ostensibly, it's to "reduce cheating", but -- as many have pointed out -- they do so in a simple-minded way that steals student work (everything students submit in the so-called "learning management systems" gets piratically stolen by the corporation and used to support their business model) and undermines the relationship between students and faculty. I use three strategies to reduce the incentives and potential for student cheating without Turnitin.

My primary goal is to have each student or group do novel projects. If work is actually novel, there are no easy candidates to cheat from. If each student (or group) is working on something unique, they can collaborate and share resources without the potential for competition or cheating to come into play. If you have students all working on identical papers (or solving "classic" problems) there is always a tempting array of examples of the "work" already done (and probably done better than any student could do it).

Second, I have students do their work in an environment where I can see the the development of the project over time. I used to use a Wiki or Drupal Revisions for this. Currently, I'm using Google Docs. This way, I can see snapshots of the project from inception to outline to finished document. I can provide feedback along the way and, in the end, have great confidence that the finished product was the authentic work of the student(s) -- much more so than if the document sprang into existence the night before it was due.

Finally, I aim to have students work on projects that are genuinely engaging. If students do authentic work that they see as valuable, there's no incentive to cheat: students will do the work because it's real work that has intrinsic merit to them.

The only reason for something like "Turnitin" is that we've created an environment where faculty have too many students to get to know them all personally. Neoliberal universities are constantly reducing the number of faculty, increasing their workload, and substituting robot labor like "Turnitin" to allowing faculty to know their students well enough to offer meaningful work and guide their writing personally. Faculty should resist the speed-up and opt-out of having their students' submissions be stolen by the parasitic corporations that aim to create a hostile environment for everyone.

Saving My Gratitude

I saw this tweet recently, which made me reflect on the question, "What should we feel grateful for?"

I've been thinking about this for a while at least in part due to watching Miss Kobayashi's Dragon Maid. There are several scenes where the characters express, what seems to me like unreasonable levels of gratitude for very small things.

I mean, anything Kanna does is sweet and charming. And it fits in well with my preferred genre of television programming: soothing shows where people are praised for doing inconsequential things. Wouldn't it be nice if we could all be so grateful for small things? But something about it niggles. Why should we have to feel grateful for stuff?

Wouldn't it be better if we didn't need to feel grateful for little things? Wouldn't it be better if the little things were taken care of, so we could free up our gratitude muscles to feel grateful for really big things?

Of course, it's a truism that you don't know what you should feel grateful for (like health) until it's gone. But I want to save up all of my gratitude for when the Mueller report finally comes out.

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