biol312

By this class, students should have completed their figure, written their methods, and had their methods followed. Usually only about 50 percent are actually there, but they're coming along.

The main purpose of this class, is to practice comparing the two figures, separating observations from inferences, and organizing RESULTS and DISCUSSION sections. For this purpose, I have collected together many examples of figures from previous semesters that they can practice on.

I've looked for a long time for an accessible reading for students to discuss the idea that observation and inference are inextricably linked. I've used an article by Fodor which was OK, but too high level. And several other things that were contextualized, but the context was too distracting. There was a nice section in Rudwick's Great Devonian Controversy that might work, but I worry that the context will still be too distracting. Instead, for the past couple of years, I've asked students to do a pre-class activity where they provide an example of an observation and inference. This has worked pretty well to get them thinking in the right direction.

I've learned to provide a little therapy up front to students before we do the practice activity. There's nothing like suddenly discovering all of the factors you never realized to control or document. Some students panic that they need to redo their figure or rewrite their methods. So I remind them that a primary purpose of the activity is to help them learn this stuff and it's OK that they didn't know it beforehand. And that if they did, we wouldn't need to do it in the first place. But it drives home the need to actually try methods out before you use them, a lesson which I hope they carry forward to their Proposals.

For the activity, I have them start to compare the figures. I ask them to remember the Writing from Experience activity: to start out just making a list of things they notice. Many students want to jump forward to conclusions like "It's a different tree"  and I ask them to back up and indicate what they can see that allows them to draw that conclusion. I wander through the room answering questions and looking at what students are recording. Then I ask them to begin to separate observations from inferences and to identify factors or variables that were different.

I provide some scaffolding along the way. First, after making a list of observations, I encourage them to try to separate their list into observations and inferences. And to try to organize the observations into an outline that presents them systematically: I ask them to recall the narrative-to-exposition activity where we came up with categories and organized their activities using a framework other than time.  Many students default to organizing around what they noticed first. Or what was the "most noticeable" difference, so I caution against these.

I also caution against making judgments: the goal is not to assign blame or say that differences are caused by errors — or to speculate about what might have happened or would happen under different future circumstances. But rather to simply observe differences and identify factors dispassionately. This is really hard.

Eventually, I ask them to present the two figures they compared side-by-side and give a quick presentation of first, just differences, and then the factors that they identified. And then I invite the other students to find other differences they might have missed.  If the class is small enough, I encourage everyone to present, but frequently the class is large enough that there really isn't time. I try to gently point out when they're describing inferences rather than observations. Or making judgments.

As we go through, I often take a few minutes to show them how to use ImageJ to collect data about differences: to measure items and to compare colors. And to emphasize that there is an immense amount of data available in the figures.

Before the end of class, I remind them that their rough drafts are due next week and that they should come to class ready to present their findings and to take notes of any feedback from the class that they can use to improve their analysis. I point out that I will start commenting on their rough drafts as soon as the next class ends and that I can give much better and more useful feedback if their manuscript is complete and as good as they can make it.

Before this class, I generally check to make sure students are posting drafts and perfect paragraphs -- and writing good comments. I try to send a quick email to students that aren't posting enough and invite them to meet with me if they're having difficulty.

By Week 3, the class is falling in a rhythm. We touch base on drafts and perfect paragraphs, review where we are on the METHODS projects and when the coming milestones happen (finish figure this week; follow methods next week; present figures & rough draft, following week; then paper due.)

I review the reading I had asked them to do and point out the section on writing an effective figure legend. And then I introduce the figure legend activity. The take-home lesson is that figures don't speak for themselves. The author needs to explain why they included the figure. And that the exact same figure might be used in multiple manuscripts for different purposes.

I digress for a bit at this point, to discuss the fact that you can't just use any old picture you find on the internet as a figure because of copyright. I gauge the audience to see who knows anything about copyright (nobody generally does). So I talk for a few minutes about copyright being enshrined in the constitution, about the original period of copyright, and if anyone knows how long it is now (and why). Then I ask about the Creative Commons and give a brief overview about how Creative Commons works, the incredible value this represents, and the importance of complying with the requirements of the licenses.

So far, I've used Flickr as a place to find Creative Commons licensed imagery for the figure legend activity. I show them how to use the advanced search to look for CC images, how to get the URL to the image file, and how to put that into a Draft post. (As I say, I've used Flickr for this for years, but their recent membership change has probably resulted in the loss of a lot of Creative Commons licensed imagery. And I can't post there anymore. So if I continue to do the activity, I'll sadly need to look for a different source of imagery.) I also show the flickr cc attribution helper as a quick way to generate the correct attribution.

For the Figure Legend activity, then, I have the students divide into pairs and find an image for which they can each write a different legend, and they each write an in-class activity with the image and their legend. I demonstrate and then help them walk through the steps. We wrap up the activity by looking at a few of the pictures they'd identified and the legends they wrote.

Subsequently, I transition to discussing multi-panel scientific figures which they will need to construct for the METHODS project. As a pre-class assignment, I had asked them to find a multi-panel figure in a peer-reviewed article and share it with me. We look at some on the screen and I ask students to explain things they liked or didn't like about them. We try to derive a list of the characteristics that make a figure effective. Some of the points I hope to make include care-and-attention to detail; having objects aligned and spaced appropriately; having consistent, high-contrast labeling, using color effectively, and considering accessibility. We also frequently discuss the ethics of manipulating imagery and that some journals require that images not be retouched or adjusted.

At some point, I ask students why there are so many multi-panel figures in scientific articles. Students generally don't know, but guess that it's to put related information together. I can generally show in one of the figures we've looked at that there is often a hodge-podge of mostly unrelated information. And I so I offer a brief lecture on the process of scientific publication and the idea of figure and color charges.

In the past, I used to demonstrate how to lay out a figure, but more recently, I've provided screencasts that the students can use for this purpose at their own pace. So, instead, I simply invite them to use the rest of the class period to work on their figures with my help, as necessary, to get their figures finished up. I remind them that, as they make their figure, they will need to be able to describe the process in their methods, so they should consider ways to make the process more replicable and to take notes they can refer to while writing their methods.

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.

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.

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.

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.