Teaching Statement development series: scientific literacy

Over the next few weeks, I’ll be sharing selected portions of my Teaching Statement here as part of a development series, as I refine my philosophies for the submission of my second-year review this fall. I welcome feedback! Feel free to comment on the post (note, all comments require my approval before appearing publicly on the site), or contact me directly if you have more substantial edits.

*Please note, these are selected portions of my Statement which have been edited to remove sensitive information. These are early drafts, and may not reflect my final version. Tenure materials that I generate are mine to share, but my department chair, committee, and union representative were consulted prior to posting these. Each tenure-granting institution is unique, and departments weigh criteria differently, thus Statements can’t really be directly compared between faculty.*


Improving scientific literacy and communication skills

In all of my curricula development, I put particular emphasis on designing assignments which build technical and communication skills. The technical skills are developed through walkthroughs for learning to use online databases such as NCBI’s Nucleotide (https://www.ncbi.nlm.nih.gov/nucleotide/) and MG-RAST (https://www.mg-rast.org/), learning to read scientific articles, and learning to analyze data as needed.  AVS 454/554 is primarily skills-based, and specific skills are listed in the Developing curricula section.

The communication skills are primarily practiced through written assignments. Scientific writing is particularly important in microbial ecology and host-microbe interactions, fields in which strict memorization might not prove useful, as the body of knowledge changes rapidly. Rather, the material lends itself to critical thinking and debating theory, to presenting a scientific argument, to problem solving, or to composing technical/scientific writing, which is different than much of the written assignments students have accomplished in other coursework. In allowing students the word count to work through their thoughts, instead of providing short answers, they are able to find the words to express their opinion on, for example, the Hygiene Hypothesis when only weeks before they didn’t know that some microbes can turn the immune system on or off. 

Written assignments allow me to provide students with more substantial feedback, including suggestions on grammatical corrections, sentence structure or placement, or leaps-of-logic where they left readers behind, and of course, on the strength of the scientific argument. This is particularly helpful when learning to write technical science.  These written assignments are narrowed to a specific topic but are otherwise open-scope, and while I provide a recommended reading list, multiple options are available for most of the lectures, which allows students to select the journal articles and scientific information used as the reference material for their assignments. In giving students the agency to choose a topic to write about from the curricula tasting menu I’ve provided in my lectures, I receive back more diverse topics than just what I provided, which keeps things interesting for me. Students are more engaged when they can connect to material of their own choosing and select something relevant to their life. And, in giving them assignments which practice their writing voice, I witness their progression towards mature scientific writing.  

For most of the students I have taught, my class is their first formal introduction to the subject, whether it be research, host-microbe interactions, or DNA data analysis. To give students more time to practice the material, and to improve retention, I give topic-related readings, have a guided discussion at the end of lectures, and ‘stack’ assignments. For example, in AVS 254, Introduction to Animal Microbiomes, students write a non-technical summary of a scientific article: 1-2 paragraph summary in which they have to introduce the paper and its purpose, the methods used, and a major result or two. Trying to explain a complex experiment in simple terms is more challenging than it seems, because students need to understand the material in order to recreate it into their own words. By restricting the length in these assignments, it forces students to be more direct in their explanation. When it comes time to write an essay for a take-home exam, I allow the students to build off those summaries, if they choose, having received my feedback.

I also promote more creative information presentation in assignments, including “concept maps”. The assignment is to create a visual outline (diagram) around the specified topic. Starting with a main idea or topic in the center, branches are created out to secondary ideas, and so on, like a spider web, to create a concept map/diagram of important related topics and information. The goal of this is to create a study guide based on what students felt are the important concepts, centered around the material we have covered in that section of the course material.  Creating a visual map in this way helps students create order out of the information, by setting up a hierarchy of importance to better understand the relationships between ideas. An example is provided below, with permission from the student.

Concept Map on ‘Microbes and Technology’, by Kiera O., student in AVS254 Fall 2020.  Used with permission.

Previous installments:

Teaching Statement development series: developing curricula.

Teaching Statement development series: accessibility

Teaching Statement development series: developing curricula

Over the next few weeks, I’ll be sharing selected portions of my Teaching Statement here as part of a development series, as I refine my philosophies for the submission of my second-year review this fall. I welcome feedback! Feel free to comment on the post (note, all comments require my approval before appearing publicly on the site), or contact me directly if you have more substantial edits.

*Please note, these are selected portions of my Statement which have been edited to remove sensitive information. These are early drafts, and may not reflect my final version. Tenure materials that I generate are mine to share, but my department chair, committee, and union representative were consulted prior to posting these. Each tenure-granting institution is unique, and departments weigh criteria differently, thus Statements can’t really be directly compared between faculty.*


Developing curricula

The first course I proposed which was accepted by the University undergraduate curriculum committee is AVS 254, Introduction to Animal Microbiomes, which I have begun teaching annually starting fall 2020.  This lecture and discussion-based course introduces students to host-associated microbiomes; the genomic collection of bacteria, archaea, fungi, protozoa, and viruses present in a host ecosystem. In each lecture, we focus on an anatomical location, theory, or a mode of microbial transfer.  We discuss the host and environmental pressures which select for the resident microbial community there, and the dynamics involved in community recruitment, function, transmission, and interactions with the host.  The material is primarily in animals, including mammals, birds, fish, amphibians, and humans, with occasional material on insects. This course is anticipated to have broad appeal to students in the School of Food and Agriculture, as well as Microbiology and Molecular Biology.  It is my hope that students are introduced to the field of host-associated microbiology through this course, and go on to participate in relevant research, during which they would generate microbial community DNA sequence datasets.  Students could then take AVS 454 in the spring of their senior year to learn to analyze this data and generate a scientific manuscript. In this way, AVS 254 sets the academic track for undergraduates to follow to learn about microbiomes from theory to application.  The course assignments feature a variety of written assignments, including ones to introduce them to online databases of microbial studies, to communicate science to the general public, and to synthesize information from various sources. The full syllabus and information about the class is relayed on my professional blog, https://sueishaqlab.org/teaching/avs-254-intro-to-animal-microbiomes/

The second, which I taught as an AVS special topics course in spring 2020, and which has been approved for spring 2021 as a formal course,  is AVS 454/554 DNA Sequencing Analysis Lab, with undergraduate and graduate sections, respectively.  This course takes students from raw DNA sequencing data through quality assurance, data interpretation, statistical analysis, and presentation of the results as a draft scientific manuscript.  Multiple drafts of the manuscript are submitted, and in addition to my reviews, students provide single-blind peer review, collectively allowing for students to refine and improve their presentation of results over time. Students are encouraged to bring their own microbial community data, or I provide unpublished data from my research collaborators, thus students have the opportunity to pursue submission of their assignment manuscripts for scientific publication along with cooperating researchers.  There is a critical need in the research community for analysis of small projects like the ones used in this class; often these data are from low-priority small projects, or researchers simply do not have the time or expertise to train students in data analysis and interpretation.  The special topics version had 7 students, with 2 additional students informally attending the class, and resulted in 3 scientific manuscripts submitted for review in fall 2020, all with student authors. The full syllabus and information about the class is relayed on my professional blog, https://sueishaqlab.org/teaching/avs-454-554-dna-sequencing-analysis-lab/

Beginning in fall 2020, I began teaching AVS 401 and 402, Senior Paper in Animal Science I and II, respectively.  Together, they form the Capstone Experience for AVS seniors.  The scope of this class was and remains: student involvement in a research project, for which students develop a research proposal in written and oral presentation formats, and then develop a research report in written and oral presentation formats. However, I developed new lectures for the class to introduce students to the proposal writing process, and research in general, as many AVS students have focused on professional applications and not on research.  These include, “What is research”, “Conducting ethical research” which also features a guest lecture from the Paula Portalain at the Office for Research Compliance, “How to read a scientific article”, “Conducting a literature review” which also features a guest lecture by Anne Marie Engelsen a Science Librarian at Fogler Library, “The proposal writing process: experimental design”, “The proposal writing process: project management.”, and “Giving a scientific presentation”. To develop their presentation skills, students first give a 3-min, non-technical “elevator speech”, then a professional presentation at the end of the semester.  To develop their written skills, students write a project summary/abstract, an outline of their proposal, and two more substantial drafts of the proposal.  For the outline and second draft, students will continue single-blind peer review of other proposals, to provide feedback and to improve their skills in science review and critique. The full syllabus and information about the class is relayed on my professional blog, https://sueishaqlab.org/teaching/avs-401-senior-paper-in-avs-i/.

The following sections detail how these curricula are developed and the intent behind assignments. 


Previous installments:

Teaching Statement development series: accessibility

Teaching Statement development series: accessibility

Over the next few weeks, I’ll be sharing selected portions of my Teaching Statement here as part of a development series, as I refine my philosophies for the submission of my second-year review this fall. I welcome feedback! Feel free to comment on the post (note, all comments require my approval before appearing publicly on the site), or contact me directly if you have more substantial edits.

*Please note, these are selected portions of my Statement which have been edited to remove sensitive information. These are early drafts, and may not reflect my final version. Tenure materials that I generate are mine to share, but my department chair, committee, and union representative were consulted prior to posting these. Each tenure-granting institution is unique, and departments weigh criteria differently, thus Statements can’t really be directly compared between faculty.*


Improving the accessibility of course materials

While course content might seem like a more pertinent place to begin this Statement, the intellectual content of a course is predicated on the ability of students to access and connect with those materials. The pandemic and social turmoil of 2020 has made this a year like no other for our students, and in conversations with them, I have gathered that it has created new challenges for them and exacerbated existing ones. The primary obstacle for students to attend live lectures and provide effort on assignments is the general increased workload related to online classes, the necessity of employment, and the inflexibility of employers who schedule student employees in a way that precludes them from attending live lectures.  Further, students are under an overwhelming amount of stress, and this has exacerbated learning disorders and created its own obstacles to engaging with course material. To that end, I have made a number of improvements in my course presentation to make materials more approachable and inclusive to learning style and student life outside of the classroom, which have been adopted in 2020 but will persist.

All the course materials for these classes are made available in Brightspace at the beginning of the semester, so students may download readings and lectures when they have access to internet services.  This also allows them to a priori assess the coursework and gauge the expectations on their time, to better plan their effort over the semester in relation to other engagements.  Assignments may be submitted early, and are accepted late with grade penalties applying in some cases.  In 2020-2021, grade penalties are waved to facilitate student scheduling during the pandemic.  For presentations, students may schedule time blocks well in advance, or may opt to record their presentation and submit videos.  Live lectures are recorded and videos are made available to students immediately after class, and previous to the pandemic I gave students the option to attend via remote video conferencing when they were home sick but did not want to miss class.

The availability of coursework in advance and the flexibility of format allows for students to engage with the work at their own pace and in a way that feels more comfortable to them.  In particular, the use of online discussion forums in Brightspace has given a voice to even the quietest of students and allowed for more diverse perspectives to contribute to the topic.

The use of online teaching platforms also allows for more accessibility in the materials for students with additional challenges. For example, after conferring with a student about understanding course materials, I added audio instructions to assignments (a recording of me reading the directions), which allows students with language dysmorphia or visual impairment to more easily understand what is being asked of them.

The use of online teaching software helps me curate assignments to more accurately test student learning and not just how clearly I asked the quiz questions.  For example, it is much easier to track student performance over time and per assignment, and assess which portions of the assignment should be revised to improve their clarity.

Finally, one barrier to student engagement in coursework appears to be a lack of student confidence stemming from an underestimation of their own agency in asking for help, accommodation, or more visibility in the class. Students appear resigned to accept a zero instead of asking for deadline extensions, or for asking for more effort from their instructor. Students appear to internalize poor performance as a personal failure, rather than a discrepancy between how the information is communicated and how it is received.  To that end, I solicit feedback using anonymous polls, and in lectures or assignments which do not generate student engagement I ask students how they would have rephrased the questions I pose to them.  

Something which I have not yet tried, but intend to implement in the future, is a self-reflection assignment at the beginning of the semester for each class. The goal is for students to feel welcome, to feel that they have agency in their education in this class, and to feel that they can let go of control in order to try something new. First, students will be asked to watch a reading of the children’s story, If You Give A Mouse a Cookie (https://youtu.be/QCDPkGjMBro), about a mouse that keeps asking for things.  Next, students will watch a TEDTalk, “Asking for Help is a Strength, Not A Weakness” (https://www.youtube.com/watch?v=akiQuyhXR8o&feature=youtu.be&ab_channel=TED). Then, students will watch the TEDTalk “The Art of Letting Go… Of The Floor” (https://www.ted.com/talks/siawn_ou_the_art_of_letting_go_of_the_floor/details). Finally, students will reflect and write down their goals for the class; 1 thing they want (the cookie), 1 thing they need (the help), and 1 thing they want to let go of (their floor).  

A series of blogs planned about developing my Teaching Statement!

One aspect of my journey in academia that I did not receive any formal training in (few do but that’s beginning to change), was the development of a Teaching Statement. Which is to say, how to develop my personal philosophy on how I approach university-level education, how I decide which facets of information or skills to include and foster in students, and how to assess whether my teaching style and content are effective.

Over the next few weeks, I’ll be sharing selected portions of my Teaching Statement here, as I refine my philosophies for the submission of my second-year review this fall. I welcome feedback! Feel free to comment on the post (note, all comments require my approval before appearing publicly on the site), or contact me directly if you have more substantial edits.

The Teaching Statement is a component for most academic positions which include a lecture or teaching component as a primary effort of the job. I had to write one for my assistant professor applications, but not for any of my post-doctoral or graduate positions even though those included some teaching. For my job applications, my Teaching Statements reflected my previous experiences, explained the courses I wanted to develop, and gave a brief introduction to how I approach teaching.

As a tenure-track assistant professor, I will spend the first 5-ish years of my position creating a tenure packet – a massive document that amalgamates all my accomplishments, failures, and explanations of my actions. Since 50% of my appointment is teaching, my packet will include student evaluations of my courses, a list and description of the courses I developed, and a detailed Teaching Statement. I will use the Statement section to outline my teaching strategies, how I implemented them at UMaine, and how I improved them over time. Since I have only been teaching for a few months at UMaine, my current Teaching Statement includes a lot of strategies which have been implemented only once so far. My Statement will refine over time as I have more to add to it, as I work out the kinks in my course materials, and as I incorporate new aspects of learning and application into my pedagogy.

Teaching Statements are not confidential (assuming they do not contain sensitive information), but are generally only shared at the request and by the discretion of the faculty member. Each tenure-granting institution is unique, and departments weigh criteria differently, thus Statements can’t really be directly compared between faculty. That being said, I thought it would be beneficial to share some of my content and the process, in part because I might as well get the extra credit for writing a blog post on content I have already generated, but also because I feel that transparency can improve my competency and academia in general.

Looking back on my first year as an assistant professor

Almost year ago, I woke up early to drive an hour and a half from the place I was staying to the University of Maine campus in Orono. My housing had fallen through after I had driven across country from Oregon to Maine, and apartments were difficult to find as students were returning for the fall semester. I took my highway exit, and almost immediately joined a mile and a half long line of cars waiting to get to campus. This may not sound like a lot, but Orono is small – really small. There are three bridges onto the island, each with a single lane of traffic in either direction. It was 8 am, and I still needed to get to campus and find parking before my 8:30 am meeting with my new department chair, something I very much did not want to be late for.

View from the bridge in Orono.

After moving only 100 yards in 10 min, I was able to turn around in a side street and get back on the highway to the next exit, in Old Town, from where I could drive southward on the island. In another 10 minutes, I had made it back to the highway, onto campus, and had found parking. That simple detour makes a nice metaphor for starting out as new faculty: there is probably an easier way to accomplish your task, you just don’t know yet that that way exists.

Last September, I joined the University of Maine as an Assistant Professor. It’s my first academic faculty position, and with it comes a variety of new responsibilities (you can read here about the differences in academic positions). There’s a learning curve to any new job, but faculty positions, in particular, require a level of expertise in time management that you likely have never encountered.

I needed to establish a laboratory and order things for it, recruit students and develop career development plans for them; develop research plans spanning the next five years; propose and then develop new classes; learn a new institutional system for ordering, reporting, teaching, advising; meet new people; and the myriad other administrative tasks that go along with teaching, advising, and managing a laboratory.

There is pressure, some from external sources but primarily from ‘the thorn in your side which seeks accomplishment’, to advance each of your goals immediately and simultaneously. You need to show progress early on, but it is not possible to devote the time and focus that each of these goals demand to all of them at once. If you try, you will find yourself buried in unmet objectives and overcooked marshmallows.

Instead, plan well in advance and try to concentrate on one objective at a time. I’ve compiled some examples, thoughts, and advice on navigating the first year of a faculty position, which is hopefully entertaining if not also useful.

Bring a campus map

One of the largest draws on my time in the first few weeks was simply finding things: buildings, services on campus, my mailbox, where the faculty parking lots were, and where the best coffee was. Make sure you have a campus map handy. I learned the hard way not to run a generic search for building names to find addresses, when I went to the wrong building which shared the name of, and was across the campus from, the building I needed to be in for a meeting. Facilities buildings can be particularly challenging to locate as they aren’t always marked, but may store excess and available office or laboratory furniture, key services, chemical supply, and more.

In addition to physical resources, I also needed to find personnel resources: who handled my startup funds? Purchasing? Hiring students? To whom do I submit course proposals? I politely framed my emails to people when fishing for the applicable administrative staff personnel, and made sure to thank them for redirecting me to the correct person.

Do not neglect the mountain of paperwork

There are so many forms you need to fill out in the first year, and you keep finding new forms as you go. I needed to sign and return my contract, funds letters, health insurance, financial conflict of interest, and more. I needed to sign paperwork to hire students, get my travel approved and more to submit my travel receipts, paperwork to propose courses, to request approval to be listed as graduate school faculty (which is not automatically conferred), and request approval to be graduate faculty in other departments or programs to be able to advise students there. You need to fill out order forms to purchase supplies, and sign off on monthly expenditure summaries. I suggest finding access to a scanner or fax, and/or software that allows you to edit and digitally sign PDFs, especially if you’ll be remote while you are trying to relocate and find housing.

Also be prepared for hours and hours of training: you’ll need to know how to use the university online system for employees, online teaching software, advising tracking programs, and any other online systems the university uses. And you need an extensive amount of compliance or professional development training your university requires, including FERPA for working with student information, OSHA and CITI safety training for working in a lab (often annual), university-based safety training for working in a lab, and implicit bias or inclusion training. Many schools also offer training in course development, and many of the other basic skills needed by professors. And be sure to keep all that paperwork, just in case you ever get audited!

Take time to generate new materials

Despite keeping copies of old protocols, lectures, and written materials that I might reuse, I found myself generating an immense amount of new written materials. While institutions often have templates available for safety materials available for use, they still require personalization to the hazards specific to the working conditions in your research location (lab, farm, field, etc.). Even the course materials that I had previously generated all needed to be reformatted and personalized to the student audiences I will have at UMaine. Here are a few examples of materials I had to generate this year:

  1. Lab safety training records (mine is a 2 page in-lab walk-through and spreadsheet linking to up to 15 other training modules)
  2. Chemical hygiene plan (how to protect yourself from the hazards in the lab)
  3. Updated lab protocols for every procedure and culture media recipe to be used
  4. Lab handbook on expectations, finding campus resources
  5. New curricula, which requires a draft syllabus, a course proposal form explaining learning outcomes and how they will be measured, not to mention the lectures, reading, assignments, and assessments to go along with it.
  6. Research proposals – by far the most intensive. I have written/co-written eight this year, ranging from one to several dozen pages in length and varying complexity.
A stack of papers facedown on a table.

Writing, especially technical writing, takes time, which was something UMaine gave me. I had almost no teaching obligation, and no undergraduate academic advising, for my first year. This gave me the opportunity to spend blocks of time focused on developing research plans that will guide me over the next 5 years, or create 15 – 40 lectures per course. This time was a luxury not afforded to all new faculty, and while you can often ask for it during job contract negotiations, many institutions pressure their new faculty to take on a lot of obligation in their first year. In that case, have as much written material ready before you begin the job would have been helpful. But, since I went from gut microbiology to soil to dust, and because I was teaching science to primarily liberal arts students, none of my old written materials were appropriate to use without some amount of revision.

Ask for help

As new faculty, you don’t yet know what to ask or who has the answer. Even finding your mailbox can be a challenge at first. Rather than waste your time trying to figure it out, doing it wrong, and then having to fix it, just ask someone for help. Portions of your funded research proposals will go to paying for administrative staff, you should use their services to help minimize the time you spend on administrative tasks. Especially since you may spend hours trying to order supplies through the university ordering system, matching receipts to expense reports, allocating expenses to different funding chartstrings, and setting up contracts with outside vendors, but you don’t get any credit in your tenure review for having spent all that time on it.

This also extends to facilities management staff, especially safety and environmental management personnel. They are the ones that have approval rights over the work you propose to do in the research spaces allotted to you. They are always incredibly enthusiastic people who value organization, preparation, and training in keeping you and your students safe on the job. If you are proactive about reaching out to them, they will generously give you their time to help you access the resources you need to be in compliance.

Ask for help even if you think you don’t need it

It’s worth putting that one twice, and it includes asking for help on course development and grant proposal writing. When you are focused on your own work, it can be difficult to review your own materials. Asking a colleague to check over your syllabus, lectures, manuscripts, or proposals can help improve their quality and save you time on revisions later. Be mindful of others’ time, but know that there are faculty who would be happy to mentor you and help you establish yourself.

Level up your time management

In part, this can be achieved by scheduling yourself in ways that make sense in the context of the academic calendar or department preferences. For example, in my current department, faculty prefer to teach Tuesday/Thursday and have meetings Mondays and Fridays. So, I asked to teach M/W/F, and will fill in meetings and advising around it. Teaching tends to interrupt the flow of my day, since I need to prepare before class and handle student queries after it. I find I work better if I stack my responsibilities which deal with communication, brain-storming, or large amounts of interaction into blocks or whole days. That leaves large chunks of uninterrupted time on Tuesdays and Thursdays to write papers, proposals, curricula, or work in the lab, while everyone else is busy with their own teaching.

Image source, Pixabay.

Leave yourself plenty of flexibility in your schedule

Avoid the temptation to schedule things as soon as possible and fill up your calendar. Especially in the first few months, you need to have flexibility in your time such that you can drop everything for a day or two in order to meet a sudden deadline you didn’t know about until it occurred to someone to tell you about it. This includes course proposals to curricula committees, which meet a year in advance of when you would actually teach the course, internal review reports, internal budget reports, and more. Don’t worry that you might delay networking with your new colleagues, people will be eager to meet and collaborate with you, you won’t have any trouble filling your dance card.

Track everything you do

Start immediately, and keep a running list of your efforts and accomplishments. All of them, no matter how small. At your annual reviews, and in particular your three-year and tenure reviews, you need to show what you have been up to and that you have been using your time effectively. You’ll never remember it all trying to write the report all at once, and you are liable to forget the smaller things. For example, in no particular order, here are the heading from my tracking list so far: advising (subset into as primary adviser and as grad committee member), publications, press releases/interviews, presentations, guest lectures, courses developed, courses taught (with number of students), professional development activities, research initiated (including student projects and things under my startup funds), proposals submitted, proposals accepted (a much shorter list), service efforts, and reviewing efforts (manuscripts, grant panels, etc.). When it comes time for me to justify myself, all I have to do is hit the “share” button.

Be kind to yourself

Despite the fact that you have been intensively training for this job for years, when you begin a faculty position you are, in a sense, starting from scratch. Most faculty have to relocate long distances to their new institution, which in itself is very disruptive and time consuming. Your laboratory space is almost always inherited from a previous lab which very likely was not specialized in what you study, and needs to be rearranged, renovated, restocked, and reenvisioned to fit your needs. This can delay your lab work by months, and if you were not provided with a lab space immediately, for years.

Most new faculty also expand their range of methodology and propose to incorporate other aspects into their research. Or, like me, have come from previous positions that were relevant, but perhaps not exactly in the same field, and need to re-acclimate and reassemble current laboratory protocols, which is time consuming. I was trained in rumen microbial ecology, but took detours into soil and indoor/building microbial ecology, as well. Even though I was returning to my primary field of experience with my position at UMaine, I still needed to remind people that I was not, in fact, an indoor microbiologist or even a soil scientist. I addressed this in the opening lines of my cover letter:

How is a rumen, a rhizosphere, and a room like a writing desk?
I have written on all of them.

You are also dropped into a thriving community of people and need to build an entirely new social network. While many faculty and graduate students will know you have arrived and reach out to you, you will need to actively recruit undergrads to your classes and your lab, as undergraduate students are not commonly involved in the interview process and won’t have an idea of your reputation or expertise before you arrive. And social interaction is tiring! You are creating new neural pathways by trying to assimilate to a new social group.

Being a new faculty member is extremely rewarding, but can also be exhausting, especially for those also trying to establish a family as well as a laboratory. Many academics report that they meet their deadlines, but fail to take care of themselves and their health and family suffers as a consequence. Take the opportunity to slow down, even if it’s just taking your laptop to a location with a better view.

View of a wooden deck with forest behind it.

5-year anniversary of my PhD graduation!

Seems like a lifetime ago that I walked the stage and was hooded during the graduation for my doctoral degree, just 5 years ago. In 2020, most Universities have cancelled their in-person graduations due to pandemic concerns, with faint hopes that they might be able to host the opportunity for 2020 graduates “to walk” at a future ceremony. It’s a good day to reflect on the opportunities and privileges I’ve been afforded that have helped me along the way.

I defended my PhD in mid March 2015, and within two weeks had driven with Lee from Vermont to Montana, flying back to VT for the ceremony in May. In those 5 years, I moved to Montana, then Oregon, then Maine; I’ve worked for 4 different departments in 3 Universities; I’ve had several different hair styles; I adopted a dog, got married, and bought a house; applied to dozens of jobs almost every year because of the short-term appointments I held; and established a research lab at the University of Maine as an assistant professor. It’s been a pretty busy 5 years, all around. I look forward to the next 5 years, and the opportunity to help the next generation of researchers begin their journey.

Perspective on developing curricula

At the University of Maine, I am currently developing two new courses based on similar material I’ve taught previously at the University of Oregon and Montana State University. I’ve written about several of those classes, including a retrospective after teaching ‘Introduction to Mammalian Microbiomes’ to humanities students. Here, with the spring semester commencing this week, I thought I would share my approaches to developing coursework. While a class doesn’t stand on organizational physique alone, it can go a long way to facilitating your communication with your students, their understanding of course expectations, and their ability to assimilate the information you are disseminating.

Organization of materials

The nature of my teaching means means that I don’t assign readings from a textbook, I curate reading lists for my students from current scientific literature, which changes a little each year. Because of this, and the need for file management, I have a few tricks. First, I have a folder (on my computer and the online teaching tool) specific to readings for that class. I curate the file name with first author, year, and few words from the title so I can keep track of what it is (ex. Zhulin_2015_databases_review). I duplicate that file name in my syllabus, so I can copy and paste instead of writing it out again.

I format my syllabus as a table, and add each reading to the day on which it is assigned. If I move lectures around, I move the whole table row, so I can migrate assignments and readings along with lecture titles. Lastly, because the readings are specific to lecture and date assigned, I mimic that order in my file names by numbering them all instead of leaving them in alphabetic order (ex. 10_Zhulin_2015_databases_review), to facilitate knowing when and which is assigned.

And I don’t just number them by order, I number them by lecture so students or I can just match the lecture number across the lecture files, assigned readings, etc.

Written assignments (when logistically possible)

A stack of papers facedown on a table.

There’s no easy way to grade written assignments from students, but I prefer it to exam-style assessments. Particularly in teaching microbial ecology and sequencing data analysis, there’s not a lot of strict memorization like there is in anatomy. The material lends itself more to critical thinking and debating theory, to presenting a scientific argument, to problem solving, or to composing mock scientific manuscripts. In allowing students the word count to work through their thoughts, they are able to find the words to express their opinion on, say, the Hygiene Hypothesis when only weeks before they didn’t know that some microbes can turn the immune system on or off.

Written assignments allow me to give them feedback, including grammatical corrections, suggestion on sentence structure, pointing out leaps of logic where they left readers behind, and of course, on the strength of the scientific argument. This is particularly helpful when learning to write technical science.

Red pen.
Photo credit: Merriam-Webster

In giving students the agency to choose a topic to write about from the curricula tasting menu I’ve provided in my lectures, I receive back more information than just what I provided, which keeps things interesting for me. And, in giving them assignments which practice their writing voice, I witness their progression towards mature scientific writing.

Stacking assignments for improved retention

It takes time to become familiar with new information. That’s why school subjects are taught multiple times, or in specific orders, as you progress through education. I have 13 – 15 weeks in a semester (or 10 in a quarter!) to on-board students and teach them a skill. For most of the students I have taught, my class is their first introduction, or their first formal introduction, to the subject.

Especially for my host-associated microbial courses, there are hundreds of years-and-counting worth of history which led us to our current understanding of the microbes that inhabit us. Without that history, an explanation of the available technology, and a discussion of how that technology shaped the view we had, I can’t do justice to the majority of the coursework where I explain how we discovered the relationship between salivation and the microbial community geography in your mouth. The first section of my ‘host-associated’ course includes this background information, and a discussion of current technology, which is reiterated when later discussing literature and how technological shortcomings can hamper our understanding of a microbial community.

To give students more time to practice the material, I give related readings, have a guided discussion at the end of lectures, and stack assignments. Students start with a non-technical summary of a paper; 1-ish paragraph where they have to introduce the paper and why it was done, the methods used, and a major result or two. Trying to explain a complex experiment in simple terms is a great way for students to gain familiarity. When it comes time to write a two-page essay for a take-home exam, I allow the students to build off those summaries, if they choose.

An inclusive syllabus

A syllabus is a document which encompasses the important information for the class, including meeting times and rooms, grading policy, lecture and assignment schedule, required reading materials, and more. It can be used to recruit students to sign up for the class, and once in attendance, it’s the first impression students have. It’s where they refer for questions about the course, what’s expected of them, and where to find instructions on assignments. I write my syllabi in a way that makes sense to me, the instructor, and I welcome feedback from students when my instructions are confusing. But, I also welcome feedback from different student populations in order to make the language and presentation of the document more approachable. Sometimes you just need something to break the ice. Like a paper turkey hat.

Sue wearing a paper hat shaped like a turkey.
Wearing the turkey hat that my mentee and I made.

I haven’t actually worn a turkey hat to teach a class, that’s too informal. I dress up like an anatomically-annotated dissected cat, because I’m a professional. Or, I ran regular class discussions that occasionally got heated and were monopolized by a fraction of the class. The next year, I took a stronger moderator stance and would impose more restrictions (“Ok the next comment HAS to use the word “microbes”). I don’t like calling on students, so the next time I have discussions I think I’m going to give them all D20 dice and have them roll for initiative on the order of presenting comments. I also added this to my syllabi:

Class participation: Students are expected to participate in discussions in class.  I strive to create inclusive discussions, but if students still find it challenging to participate please notify me and I will alter the discussion format as needed.

AVS 590 Syllabus spring 2020

Most universities also require text or links to their campus policies, driven by federal, state, or university law. These include a statement about accommodations for disabilities, although many faculty are happy to make accommodations without the student receiving prior approval. I started allowing students to occasionally attend lectures by video conferencing, if they notified me ahead of time. It allowed students who were ill or traveling to keep pace with the material, and I have even remotely conference-videoed in to a student’s laptop to present when I was home sick but didn’t want to cancel class.

New this year, I’ve included text about students missing classes for parenting or caregiving responsibilities, something I don’t currently participate in, so it was not something I thought to include information on until someone else (Jenn Perry) gave me their perspective. Now I have this:

Pregnancy, lactation, and parenting: I am happy to make accommodations for students based on pregnancy, lactation, and parental needs, as well as work with the Office of Equal Opportunities. Maine state and UMaine policy allows students to breastfeed in any space, including in class. If a lactation space is required, please contact E.O. for arrangements.

AVS 590 Syllabus spring 2020

Similarly, a tweet by Dave Baltrus about including inclusive statements such as information for food insecure students led me to add this:

Food insecure? Need clothes? Check out the Black Bear Exchange’s Food Pantry: https://umaine.edu/volunteer/black-bear-exchange/ or Old Town Crossroads Ministry.

AVS 590 Syllabus spring 2020

And finally, I added text about mandatory reporting. As a public university employee, I am obligated to notify the University of Maine Title IX office about criminal actions towards or by anyone on campus. If a student reveals information to me, I have to pass it on to the Title IX office which will then discretely reach out to the student with resources. The office advocates for anyone on campus, but they are particular important in situations involving students who are low on the power scale and cannot advocate for themselves. While my door is always open to students looking for help, I felt it was important for them to know that I might not be able to keep the meeting confidential.

Inclusiveness in the classroom is important to me, because if students don’t feel welcome, comfortable, and free from hunger, they can’t learn. Despite what opponents think, this doesn’t involve “coddling” or “being too soft”. It means being realistic in my expectations about how people learn and what else they are dealing with that might be inhibiting that. It means that I learn to be more proficient at communication and personnel management, which are vital skills for academics. And it means that we all elevate our skills together.

Silhouettes of four people jumping in a dark cave.

AVS 254: Introduction to Animal Microbiomes

My first official course at the University of Maine has been approved! Starting Fall 2020, I will teach AVS 254: Introduction to Animal Microbiomes!

This 3-credit course is geared towards undergraduates with a science background, with sophomore status or higher. Some familiarity with microbiology, genetics, mammalian anatomy, or microbial ecology would be helpful, but is not specifically required.

The working syllabus can be found here, with more information on lectures, assignments, workload, classroom policies, and more:

Description:  This course introduces students to host-associated microbiomes; the genomic collection of bacteria, archaea, fungi, protozoa, and viruses present in a host ecosystem. In each lecture, we will focus on an anatomical location, and discuss the host and environmental pressures which select for the resident microbial community.  The material is primarily in animals (mammals, birds, fish, amphibians) but includes some human-specific comparisons. This course will introduce ecological theories (e.g. environmental selection, neutral theory) in the context of microbial communities, the history of host-associated microbiology, and how technology has contributed to or limited our understanding of organisms and their critical role in our health and development. The skill-set objectives include group discussions, reading scientific literature, and scientific writing in a variety of styles and both technical and non-technical formats. 

DNA double helix with dollar signs as a nucleotide.

The cost of scientific publishing

I’ve published a lot this year. More than normal, since I had 5 months with extra time and the knowledge that I would not be able to devote time to old projects if I began a tenure-track position. It’s been wonderful to publish so many projects, especially ones that had been languishing. But publishing fees can be steep, and often the grant is spent out by the time you publish, leaving researchers struggling to pay to get their results out. The more prestigious the journal, typically; the higher the cost. This encourages many authors to turn to lower impact or less reputable journals, which in turn causes colleagues to be suspicious of the article and may hurt their ability to get more grant money or promotion. On top of the base article processing charge (APC), there may be additional fees to print color photos, supplemental information, or to make the article open-access (readable without a journal subscription).

I’ve published 10 articles in 2019, only a fraction of what I contributed to paying for (thank you, collaborators!!). All costs are presented as 2019 fees in USD. Some journals charge less if you are a member of their society, or have financial assistance, but I’ve included the prices we paid.


Animal: $2835 APC flat rate (includes open-access)

Basic and Applied Ecology: $2000 APC for non-members (includes open-access)

Buildings: $1006 APC (always open-access)

Geoderma: $3350 APC for open-access and $2052.30 for printing 6 figures in color.

Indoor Air: $4300 APC for open-access

Journal of Animal Science: $1300 APC ($100/page member price x 10 pages + $500 color figure charge)

Journal of Exposure Science and Environmental Epidemiology: $3760 APC (includes open-access)

PeerJ: $1095 APC (always open-access). PeerJ also gives discounts for acting as a reviewer, though not applied here.

PLoS Biology: $0 APC for essays because they are published in the magazine (always open access)

PLoS ONE: $1595 APC (always open-access)

Total cost: $21,241


Keep in mind, I’m an editor for two journals and a reviewer for over a dozen, none of which I get paid for. Initial reviews take 2-4 hours, and follow up reviews on revised manuscripts can take 1-2 hours per revision (usually no more than 2 rounds). Editorial takes 1-2 hours per manuscript total, depending on the ease of finding reviewers and the completeness of those reviews. I estimate I’ve provided $3,240 (net) in editorial and review services this year alone.

It takes a village to write a scientific paper

Every scientist I know (myself included) underestimates how long it will take to write, edit, and submit a paper.  Despite having 22 publications to date, I still set laughably-high expectations for my writing deadlines.  Even though scientists go into a project with a defined hypothesis, objectives, and workflow, by the end of data analysis we often find ourselves surprised.  Perhaps your assumptions were not supported by the actual observations, sometimes what you thought would be insignificant becomes a fascinating result.  Either way, by the time you have finished most of the data analysis and exploration, you face the difficult task of compiling the results into a meaningful paper.  You can’t simply report your data without giving them context and interpretation.  I’ve already discussed the portions of scientific manuscripts and how one is composed, and here I want to focus on the support network that goes into this process, which can help shape that context that you provide to your data.

One of the best ways in which we can promote rigorous, thoughtful science is through peer-review, which can take a number of forms.  It is worth noting, that peer-review also allows for professional bullying, and can be swayed by current theories and “common knowledge”.  It is the journal editor’s job to select and referee reviewers (usually 2 – 4), to compile their comments, and to make the final recommendation for the disposition of the manuscript (accept, modify, reject).  Reputation, and personal demographics such as gender, race, or institutional pedigree can also play a role in the quality and tone of the peer-review you receive. Nevertheless, getting an outside opinion of your work is critical, and a number of procedural changes to improve transparency and accountability have been proposed and implemented.  For example, many journals now publish reviews names online with the article after it has been accepted, such that the review does not stay blind forever.

Thorough reading and editing of a manuscript takes time.  Yet peer-reviewers for scientific journals almost unanimously do not receive compensation.  It is an expected service of academics, and theoretically if we are all acting as peer-reviewers for each other then there should be no shortage.  Unfortunately, due to the pressures of the publish-or-perish race to be awarded tenure, many non-tenured scientists (graduate students, post-docs, non-tenure track faculty, and pre-tenured tenure-track faculty) are reluctant to spend precious time on any activity which will not land them tenure, particularly reviewing.  Moreover, tenured faculty also tend to find themselves without enough time to review, particularly if they are serving on a large number of committees or in an administrative capacity.  On top of that, you are not allowed to accept a review if you have a conflict of interest, including current or recent collaboration with the authors, personal relationships with authors, a financial stake in the manuscript or results, etc.  The peer-review process commonly gets delayed when editors are unable to find enough reviewers able to accept a manuscript, or when reviewers cannot complete the review in a timely manner (typically 2 – 4 weeks).

I have recently tried to solicit peer-review from friends and colleagues who are not part of the project before I submit to a journal.  If you regularly follow my blog, you’ll probably guess that one of the reasons I do this is to catch spelling and grammatical mistakes, which I pick out of other works with hawk-like vision and miss in my own with mole-like vision.  More importantly, trying to communicate my work to someone who is not already involved in the project is a great way to improve my ability to effectively and specifically communicate my work.  Technical jargon, colloquial phrasing, sentence construction, and writing tone can all affect the information and data interpretation that a reader can glean from your work, and this will be modulated by the knowledge background of the reader.

I’ve learned that I write like an animal microbiologist, and when writing make assumptions about which information is common knowledge and doesn’t need a citation or to be included at all because it can be assumed.  However, anyone besides animal microbiologists who have been raised on different field-specific common knowledge may not be familiar with the abbreviations, techniques, or terms I use.  It may seem self-explanatory to me, but I would rather have to reword my manuscript that have readers confuse the message from my article.  Even better, internal review from colleagues who are not involved with the project or who are in a different field can provide valuable interdisciplinary perspective.  I have been able to apply my knowledge of animal science to my work in the built environment, and insights from my collaborators in plant ecology have helped me broaden my approach towards both animals and buildings.

No scientific article would be published without the help of the journal editorial team, either, who proof the final manuscript, verify certain information, curate figures and tables, and type-set the final version.  But working backwards from submission and journal staff, before peer-review and internal peer-review, there are a lot of people that contribute to a scientific article who aren’t necessarily considered when contemplating the amount of personnel needed to compose a scientific article.  In fact, that one article represents just the tip of the iceberg of people involved in that science in some way; there are database curators, people developing and maintaining open-source software or free analysis programs, laboratory technicians, or equipment and consumables suppliers.  Broadening our definition of science support network further includes human resources personnel, sponsored projects staff who manage grants, building operational personnel who maintain the building services for the laboratory, and administrative staff who handle many of the logistical details to running a lab.  It takes a village to run a research institution, to publish a scientific article, to provide jobs and educational opportunities, and to support the research and development which fuels economic growth.  When it comes time to set federal and state budgets, it bears remembering that that science village requires financial support.

 

Featured Image Credit: Kriegeskorte, 2012