Teaching Statement development series: science and society

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.*


Tying science course content to other aspects of society

I have two goals in my attempt to connect my science curricula to other aspects of society: to provide a broader educational perspective on science, and to stimulate imagination regarding the application of scientific knowledge to community building and civic engagement. Students need to understand that science is ongoing, and that there are yet many questions in the field for them to answer.

One technique to connect science and society in my coursework is to encourage students to self-identify as scientists, and to understand that they are able to participate in it. For example, on the first day of AVS 401 (Capstone), the students made a word-cloud of adjectives to describe their idea of a scientist, shown below.  At the end of the academic year, after participating in research and learning about the process, students will make another collaborative world-cloud.  As a class, students will reflect on whether their understanding of science and scientists has changed, and whether they are more (or less) likely to perceive science as a field that they are able to engage with.  Hopefully, this participation in research and reflective exercise will accentuate their use of effort-based descriptors, such as “patient” or “methodical”, rather than ability-based descriptors, such as “gifted”, when thinking about scientists, and thereby when thinking about themselves.  It is important for students to learn that science is a process to participate in, not a gift that you are born with.  In fact, a large-scale research study found that student achievement gaps were more dramatically narrowed when the instructor held the personal view that ability could be taught, rather than ability was fixed, i.e. you are born with it  (Canning et al. 2019, DOI: 10.1126/sciadv.aau4734).

Word-cloud of adjectives to describe a scientist, AVS 401, Sept 1, 2020.

Another technique is to highlight the importance of the principles of research (i.e. finding and testing information for accuracy) and how those principles can be integrated into daily life or future careers, regardless of what those are. This includes teaching the AVS 401 students about why we need research, for example, in order to be more objective and remove our personal biases.  I explain how search engines work, and how the design of algorithms can contribute to the popularity of search results outweighing the quality and correctness of the information.  I talk about the importance of unbiased data in training sets, highlighting examples of artificial intelligence programs which were trained on social media interactions espousing violent rhetoric because human users thought it was fun to tell the AI that all humans held such views. 

In addition to providing information about the process of research and how to design an experiment, I give AVS 401 students information on the administrative aspects of research, including personnel and project management.  For example, I teach students about how researchers find funding and the goals of writing research proposals, and highlight the importance of including descriptions of project management in research proposals to prove you have the capacity to perform the experiment  I also give examples of demonstrated implicit bias in proposal reviewing that creates inequality in funding availability to different demographics of scientists, and how this artificially makes them look less competent when it comes time for internal review.  While this may seem immaterial to the class, reminding students that science cannot be divorced from the views of society, and that in order to overcome our bias as scientists we need to overcome our bias as people, too.

Thus, I provide background information of science and society to my classes, where pertinent.  For AVS 254, Introduction to Animal Microbiomes, the first section of the course (8 lectures) are devoted to the development of microbial ecology theory and technology over time, from the discovery of “wee animalcules” to the use of metagenomics. During these lectures, I provide annotations on historic scientists who have been lauded for their work, but who used that science for discrimination.  For example, James Watson, one of the researchers credited with determining the structure of DNA and the process of replication, was famously racist, sexist, and anti-Semitic, to the point where some of his awards were later revoked by institutions.  In one of his biographies, he devoted an entire paragraph to denigrating the appearance of Rosalind Franklin, whose originally-uncredited work was integral to Watson’s own success (https://www.vox.com/2019/1/15/18182530/james-watson-racist).  By telling this story in lecture, and following up with a discussion on “Elitism and Credit for Intellectual Contribution”, I place what is clearly a monumental scientific discovery in the context of society and human interactions.  It is critically important for students to understand that the journal articles they read about animal microbes in the rest of the class is the result of hundreds of years of effort and thousands of contributors, because it starts a discussion about power dynamics in science and in workplaces, in general.  It is important for them to understand how implicit bias, stereotypes, elitism, or even poor interpersonal relationships can affect science, as well as for them to learn that they have rights to their intellectual property and that they can actively make their future workplaces more equitable such that we do not continue to make the mistakes of the past.

Another technique is getting students to appreciate the hundreds of years-and-counting worth of history which led us to our current understanding of the microbes that interact with us. Without that history, and a discussion of how that technological journey shaped our current scientific understanding, I cannot do justice to the majority of the coursework. By and large, DNA sequencing is the technology behind much of the subject material in my AVS 254, Intro to Animal Microbiomes class. Sequencing is often portrayed as a panacea for all scientific questions, yet I teach students that as this technology improved we realized our experimental procedures were biased.  Being able to see this change over time requires perspective and time spent in a field, something that most undergraduates do not yet possess for microbial ecology.  And without the historical perspective, how can we understand that the most prevalent DNA sequencing technology today owes its success, in partm to the acquisition of a patent the company bought in a ‘fire sale’ because no one wanted to buy the patent outright from an African American with no higher education degree. In science courses, we only have so much time to disseminate information, and for that reason we often skip to the results, the end point, the cutting edge. Yet in telling only one story, or only the ending of the story, we rob students of the opportunity to see that science is a living process over time.  To see that scientists may be fallible, or that technology has both limited and informed our understanding of the natural world, or to understand why “some scientists” may disagree about the effects or scope of climate change.  Students need to understand that science is ongoing, and that just because knowledge is not fixed does not mean that is unreliable.

Towards the second goal, I use assignments and in-class discussions to stimulate imagination towards applying scientific knowledge to life outside of the classroom for the purpose of community building and active citizenship. In fact, the AVS 254 discussion on “Elitism and Credit for Intellectual Contribution” is a great example. Students engage with this topic because it is a situation that they can identify with. An in-class discussion on “Are your microbes really yours?” similarly stimulates student engagement. I think this topic succeeds because it is a novel concept and it sparks curiosity, and because it is a neutral topic in that there is no wrong stance, and asking questions about the topic is not associated with a moral judgement.

However, not all topic discussions are successful with all student groups.  For example, “Do we have a right to tell people how to conduct agricultural practices?”, after a lecture about agricultural practices which affect gut microbes and may trigger disease in livestock  This topic is one that I had devised at the University of Oregon for non-science-majors, who were interested in human connection to animal-microbe interactions.  Asking them questions which deliberately set up a pro/con side appealed to them because they were used to being asked to debate stances they did not espouse and they found it an interesting thought experiment.  However, at UMaine, teaching to animal- and life science students, the same question failed to engage them because the topics were not hypothetical as they had direct experience in it and they had already formed conclusions about the topic.  UMaine students also felt that the phrasing of this question was insensitive, which had been my point – I wanted them to practice arguing a stance for agricultural sustainability in the face of opposition.  Because UMaine students had already come to the same conclusion about this topic – that agricultural sustainability was important and could be used to improve economic security of food systems, they felt there was no question for them to answer.  

As my first semester teaching AVS 254 has been fall 2020, in a remote format during a pandemic, the conversational interaction that I typically have with my students is lacking, which is usually the basis for how I develop the topic and phrasing of discussions. Instead, to improve my curricula and my strategy for using discussions to improve student critical thinking skills over the course of the semester, I workshopped my approach to discussions in an ad hoc Pedagogy in STEM working group on campus.  The working group meets semi-weekly to discuss curriculum development, and in particular, weaving social issues into science courses. I led a one-hour meeting on re-thinking tense classroom conversations, as well as making student contributions equitable and productive during discussions. My re-devised strategy (a direct result of that working-group meeting) for discussion topics which do not elicit student engagement is to ignore the topic discussion and jump to resolution planning in the short and long-term using starting scenarios which include cost/benefit analyses, if applicable.  Instead of “Do we have a right to tell people how to conduct agricultural practices?”, the set-up will be “How do we plan for more sustainable ruminant agriculture?”  Students will be given a scenario of a farmer in Florida that wants to switch their cattle herd to a heat tolerate breed.  A brief economic analysis will be provided, such as cost to buy new cattle, as well as management concerns such as availability of markets to sell off current stock or sourcing new animals from less-common breeds.  Students will then have to decide how they will “get there from here”: what will they do today? Tomorrow? In one year? In ten years?  Changing industries and human societies is a slow path, and many people get discouraged by their lack of progress and move away from active citizenship.  Having students plan out short and long-term goals for change will ideally help them to learn to apply knowledge to planning actions today, and in the future.


Previous installments:

Teaching Statement development series: research mentorship.

Teaching Statement development series: research and education.

Teaching Statement development series: scientific literacy.

Teaching Statement development series: developing curricula.

Teaching Statement development series: accessibility.

Teaching Statement development series: research mentorship

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.*


Research mentorship (modified to remove sensitive information)

For students in my lab, who are listed in the Student Research Mentoring section, I approach mentorship the same way I do my in-class pedagogy, which is to say that I stress the importance of both technical skills and communication skills.  A large portion of their time is spent developing laboratory skills, many of which are translatable to other fields and types of research.  These skills include sample collection, DNA extraction, polymerase chain reaction (PCR), qualitative PCR (qPCR), DNA purification and quantification, gel electrophoresis, DNA sequencing library preparation, DNA sequence data analysis, microbial isolation from mixed communities, microbial culture under aerobic and anaerobic conditions, microbial biochemical testing and microbiology, microscopy, as well as some mammalian cell culture.  In addition to learning these skills, students are responsible for performing related data analysis, developing or refining protocols, and learning to care for the equipment they are using. As for communication skills, students must read and translate information found in scientific articles, perform literature reviews, present their updates or results in lab meetings, write scientific protocols, generate and give scientific presentations, and write scientific manuscripts or other documents for dissemination.

However, I feel that learning to manage scientific research is also a critical skill for students, and all participate to some degree, including my undergraduate students. Students are asked to take the lead on contacting other faculty with questions, calling manufacturers for information on supplies and reagents, generating shopping lists for materials and comparing products, updating inventory, and sharing and curating information or data. Once students feel proficient in a particular skill, they are encouraged to teach it to another student.  Likewise, multiple students are grouped together on projects, giving them a cohort of peers to trouble-shoot and discuss their research with.  For projects involving culturing work, this also requires them to learn division of labor, time management, and coordination of research efforts in order to maintain the experiment and share equipment.  For graduate students, these project management skills also include a small amount of personnel management, as they are designated as project team leaders and participate in coordinating undergraduate students in the lab.

I have been mentoring student researchers at the University of Maine since January 2020, beginning with undergraduates and a non-thesis graduate student, and adding two thesis-based graduate advisees as of fall 2020.  I am currently a documented committee member for three graduate students, including two in the School of Food and Agriculture, and one at Montana State University in Land Resources and Environmental Sciences.  For each of these students, I provide mentoring, training, and high-level perspective on microbiology lab work, including DNA extraction, PCR, qPCR, and sequencing library preparation, as well as DNA sequence data analysis. All three projects relate to my work on microbial communities in agriculture, or which would impact the gut. Several of these students are working on collaborative projects between myself and other researchers, including those on and off campus.  In particular, students from other majors and departments bring their scientific skills to my microbiology and microbial genetics work, and increase the overall competency and skill set of my lab. These students support interdisciplinary work, and have contributed or will contribute to scientific publications and presentations as authors. 

I strongly believe that students who contribute to research should have the option to contribute at an author level, if they choose, but many are unaware of their intellectual property and publication rights that the University supports.  In my varied experiences in academia, I have been witness to research disputes on authorship which inevitably ended in the student researcher being negatively affected by the resolution of the dispute.  In nearly all of these cases, guidelines on publication rights and expectations in the lab were not clearly outlined between the student and the advisor.  Nor were there guidelines in place for resolving disputes via mediation from a true third party. In one of the labs I trained in, a Memorandum of Understanding was developed by the researcher to outline rights and responsibilities for new lab members, and over the years I adopted this document to be pertinent for my research situations.  At the University of Maine, I heard a similar need for this type of document from students, and have been working with students, faculty, and administrative staff to revise an MOU for use on campus.  At present, we are in the process of finalizing a clear first draft, after which we will invite campus members, such as those in the Graduate College, unions, tech-transfer office, and Student Life, to a focus group to discuss the document. It is my goal to have the Graduate College adopt a modifiable version of the MOU and encourage faculty to discuss it with new lab members.

[The rest has been removed for this post as it contains student information.]


Previous installments:

Teaching Statement development series: research and education.

Teaching Statement development series: scientific literacy.

Teaching Statement development series: developing curricula.

Teaching Statement development series: accessibility

Teaching Statement development series: research and education

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.*


Integrating research and teaching

AVS 454/554 DNA Sequencing Analysis Lab encourages students to bring their own microbial community data, or allows them to work on unpublished data donated by my research collaborators.  By working with unpublished data, and connecting to active research projects,  students have the opportunity to develop real-world skills in a lifelike research context.  While I teach them how to perform statistics or create figures, as well as when they are contextually appropriate, the development of their research narrative and results presentation is somewhat-student led.  They learn to explain their data, not only to me or to other students during peer-review, but to researchers who typically have expertise in fields other than microbial ecology.  And, the use of unpublished data creates the possibility to pursue submission of their manuscripts, generated for class assignments, for scientific publication along with cooperating researchers, which engages students in research beyond the scope of the class.  

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 (AVS 590) in spring 2020 was composed of 7 students, with 2 additional graduate students informally attending the class as they were graduating that semester.  The work in class resulted in 3 scientific manuscripts submitted for review in fall 2020, all with student authors and some with student first-authors. In particular, the extended interactions of students through internal and external review offers them an opportunity for guidance through what can be a challenging process for new researchers. For the spring 2020 class, I was presented with two unpublished datasets from collaborators at UMaine and across the US, and I view this class as an opportunity to assist UMaine students in networking to improve their career trajectory. I anticipate more enrolled students, and more collaborative projects, in future offerings of this course.

 Beginning in the 2020/2021 academic year, I began teaching AVS 401 (fall) and 402 ( spring), 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. Animal and Veterinary Science is heavily focused on professional development for animal science, production, and veterinary careers, which most accurately serves the interest of the majority of our students.  The final component of their education with us is to learn to apply that knowledge in an informational-seeking capacity, i.e. research.  Most students in the department and on campus, in general, have no prior experience participating in research. Or, their participation extends to sample collection and processing, and data analysis.  It is difficult to incorporate the aspects of experimental design conceptualization and project management, despite being critical aspects of scientific research and development.  Thus, in fall 2020 I began with an academic approach to applying these aspects of research in education, through the use of lectures.  Feedback from students early on in the fall semester indicated that many of the concepts I included in my lectures (see Developing curricula section) were almost or completely new to them. 

To provide a more comprehensive experience in conceptualizing research questions and developing plans to test them, I required students to include other components in their research proposals in addition to the background information, hypothesis, objectives/aims, and experimental design or project description.  These additional components include a project timeline, a list of project personnel and their responsibilities or contributions, a statement on data management and sharing, and a statement on information dissemination and sharing, with specific outcomes or outputs listed (if applicable). The infection-preventative measures enacted to contain the SARS-CoV-2 pandemic has shifted the amount and type of research on campus, and the way that students are able to engage in active research.  Thus, for fall 2020 I did not require students to consider some aspects while writing their research proposal in the fall for AVS 401, such as budgets and justification, whether they had available equipment, and a description of their available facilities, but these will likely become small written components in future years.  For the research proposal, I do not consider any of the materials that students generate to be binding, as projects evolve during their course and many student projects are redirected by advisors, and I clarified this point to students.  As long as a research proposal was well-thought out, it could be materially different from the research report they generate by the end of the spring semester.


Previous installments:

Teaching Statement development series: scientific literacy.

Teaching Statement development series: developing curricula.

Teaching Statement development series: accessibility

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).  

Microbiomes Across (Agricultural) Systems

Beginning in early 2019, I participated as one of the guest editors for the Microbiomes Across Biological Systems special call hosted by three PLoS Journals. The journal collection was officially released in early 2020, but due to the global upheaval this year, the overview piece planned by the guest editors was not able to be completed. Here is a partial overview, written by myself and written by Dr. Noelle Noyes, Assistant Professor at the University of Minnesota.

Diet and gut systems

Ecosystem dynamics are important at any scale

As humans, animals, and plants are key members of their environmental ecosystems, so too are microorganisms key members of the host-associated ecosystems in which they reside.  Throughout eons of interactions between microorganisms and macroorganism hosts, specialized and reproducible host-microbial interactions developed, leading to inherent differences in the microbial communities residing within even closely-related microorganism hosts (Bennett et al. 2020; Loo et al. 2020; Sun et al. 2020).  The strength and outcome of each of these host-microbial interactions can sway the trajectory of that host’s life, and decades of research has only barely uncovered the mechanisms behind the exorbitantly complicated relationships between host and microbial community.  In part, this is because the host microbiome does not develop in isolation; it is dependent on the environment (e.g. Bennett et al. 2020), on diet (e.g. Taylor et al. 2020), on the host signalment (e.g. Jacobs et al. 2020), and upon all the minute details of that hosts’s life which informs the “who”, when, why, and how of host-microbial interactions. To better understand biological systems, we must evaluate them at different scales, from the microbial ecosystems to the environmental ones, and how microbial selection and transfer are the mechanisms by which these scalable ecosystems are connected.

Your gut microbiota are what you eat

Diet is the most consistent and striking aspect of a host’s lifestyle which can select for different microbial communities in the gastrointestinal tract (Bloodgood et al. 2020; Loo et al. 2020;  Lü et al. 2020; Ogato et al. 2020; Sun et al. 2020; Taylor et al. 2020), and especially at different locations along the GI tract depending on localized anatomy and organ-specific environmental conditions (Subotic et al. 2020; Lourenco et al. 2020).  The amount of different macronutrients, such as proteins, fats, or carbohydrates, in a diet selectively encourage different biochemical capabilities in the gut microbiome and the microbial members which can thrive under those conditions (Lourenco et al. 2020).  At a finer resolution, the specific types of each nutrient, and their availability for catabolism will also affect the gut microbiome (Taylor et al. 2020).  

Yet, diet may affect the microbiome of different host species in nuanced ways, based on dissimilar anatomy of the gastrointestinal tract, the relative stability of host-microbial interactions and host reliance on their gut microbiota, and the relative stability of the diet of the host. For example, specialized herbivores which possess a four-chambered stomach, known as ruminants, are dependent on the presence of fibrolytic microbiota, yet due to the overwhelming microbial diversity present in their GI tract they have functional redundancy which allows for a great deal of latitude in the specific microbial species present in their communities.  Microbiota in the rumen of cattle are easily swayed by changes in diet composition (Lourenco et al. 2020; Ogato et al. 2020), as were microbiota in sea turtles (Bloodgood et al. 2020) and potato ladybird beetles (Lü et al. 2020), whereas diet composition seems to affect only the less abundant community members in the honeybee gut (Taylor et al. 2020).  

The impact of diet on the gut microbiome and host health is an active and long-standing research field, yet the depth and breadth of dietary effects leaves many questions yet unanswered, particularly in cases where feeding the animal host is prioritized over feeding the gut microbiota specifically.  Animal production and weight gain is a primary goal of feeding strategies in agriculture, often with detrimental effects to the functionality of gut microbiome which can lead to systemic health problems in the animal if the perturbation to the microbiome is extensive or protracted. An understanding of how host-microbial ecosystems can be altered over time to prevent such health problems is important (Ogato et al. 2020). Similarly, wild animal recovery programs opt for diets to support weight gain in malnourished animals, even when the diet composition is contrary to their natural diet. In recovering juvenile sea turtles, feeding an omnivorous diet to promote weight gain over the herbivorous diet these turtles consume at this stage of life causes changes in gut microbiota profiles and it is unknown how this may affect long-term digestive function and health (Bloodgood et al. 2020).

An interesting and understudied aspect of the effects of diet on the gut microbiome is the potential for knock-on effects across microbial ecosystems.  For example, changing the diet may impact the gut bacterial profiles based on “who” is directly catabolizing those nutrients, but may also impact other microorganisms which are supported by the byproducts of that microbial digestion.  Similarly, therapeutics targeting some microbial community members may inadvertently alter other community members.  A deeper understanding of how diet and medication affects the entire microbial community and not just selected members can reveal insight into community dynamics and the relative risk of medications to cause disruptions.  For example, anthelmintic in beagles were shown to not alter fecal microbial communities (Fujishiro et al. 2020).

Environment to host to host: microbial transfer highlights connections between systems

Yet, what constitutes a beneficial microbiome for one animal species may be detrimental to another animal species. A dramatic example of this is vector-borne infectious disease, in which symbiotic or neutral members of an insect microbiome are highly pathogenic in other animals which have not learned to tolerate or control those particular microorganisms. Bacteria carried by arthropods, such as mosquitos, flies, or ticks, may provide nutrition or disease-mitigation benefits to its arthropod host yet cause widespread disease and mortality in humans and animals (Bennett et al. 2020). Interaction with the ecosystem can recruit microbial members to a host-associated microbial community.  Habitat destruction alters the quality of the environment and thus microbial transfer from environment to insect, and this can make arthropod microbial communities more variable (Bennett et al. 2020). It is yet unknown if these knock-on changes to the arthropod microbiota will have positive or negative impacts for vector-borne diseases.  

Studies such as Bennet et al. (2020), which put host-associated gut microbial community assessment into the context of habitat quality and environmental microbial transfer, remind us that microbial communities do not exist in isolation.  Understanding how the environment shapes the microbial communities which shape the host is a critical aspect to understanding the connectedness between biological systems.  Further, it better illuminates the dynamics of microbial transmission and when they are and are not transferred.  Maternal transfer is a well-demonstrated mechanism of vertical transmission of microorganisms, and transfer between social pairs is a method of horizontal transmission of microorganisms, both often demonstrated via microbial community similarity analysis.  However, when pair-bonded tree swallows are sampled asynchronously, there is no significant level of similarity in their gut microbiota (Hernandez et al. 2020).

The need to put host-associated gut microbial community assessment into the context of environment is also highlighted in Loo et al. (2020), in which habitat and geographic location impacted the gut microbiome of island finches independently of foraging diet data. Environmental conditions, localized plant diversity, and localized niche competition can also impact the type, nutritional content, and life stage of plant life, which can in turn impact the gut microbiota recruited in those host animals consuming plants.  As discussed in Jacobs et al. (2020), when animals are removed from their natural environments and held in captivity, where local macro-biodiversity is dramatically reduced, there is often a corresponding decline in host gut microbial diversity which can impact animal health.  In semi-captive situations, such as beehives, animals may still freely encounter diverse environmental microorganisms, but the habitat or housing design may impact host behavior and/or stress response due to interactions with humans.  Chronic stress has been demonstrated to negatively impact the diversity and functionality of host-associated microbial communities in the gut by altering the host immune system and its latitude for microbial tolerance. Thus, even at the very localized scale, environmental conditions and habitat play a role in host-microbial interactions (Subotic et al. 2020).

Featured papers, which can be found here.

  • Bennett et al. Habitat disturbance and the organization of bacterial communities in Neotropical hematophagous arthropods
  • Bloodgood et al. The effect of diet on the gastrointestinal microbiome of juvenile rehabilitating green turtles (Chelonia mydas)
  • Fujishiro et al. Evaluation of the effects of anthelmintic administration on the fecal microbiome of healthy dogs with and without subclinical Giardia spp. and Cryptosporidium canis infections
  • Hernandez et al. Cloacal bacterial communities of tree swallows (Tachycineta bicolor): Similarity within a population, but not between pair-bonded social partners
  • Jacobs et al. California condor microbiomes: Bacterial variety and functional properties in captive-bred individuals
  • Loo et al. An inter-island comparison of Darwin’s finches reveals the impact of habitat, host phylogeny, and island on the gut microbiome
  • Lourenco et al. Comparison of the ruminal and fecal microbiotas in beef calves supplemented or not with concentrate
  • Lü et al. Host plants influence the composition of the gut bacteria in Henosepilachna vigintioctopunctata.
  • Ogato et al. Long-term high-grain diet altered the ruminal pH, fermentation, and composition and functions of the rumen bacterial community, leading to enhanced lactic acid production in Japanese Black beef cattle during fattening
  • Subotic et al. Honey bee microbiome associated with different hive and sample types over a honey production season
  • Taylor et al. The effect of carbohydrate sources: Sucrose, invert sugar and components of mānuka honey, on core bacteria in the digestive tract of adult honey bees (Apis mellifera)

Water systems

written by Dr. Noelle Noyes, University of Minnesota

Environmental and physiochemical factors structure water-associated microbiomes

Water bodies are highly diverse ecosystems, and this is reflected in the articles of this Special Edition, which investigate the microbiomes of Indian mangroves, Icelandic cold springs, Antarctic lakes, urban lakes in Beijing, and Pacific seawater. A common theme emerging from this diverse collection is that water-associated microbiomes are highly influenced by the nutrient and physiochemical properties of the water body itself; and that these properties, in turn, are influenced by the surrounding atmospheric and environmental inputs. For example, nitrogen levels were correlated with microbial composition in Mangrove-associated and Beijing urban lake water samples (Dhal et al 2020, Wang et al 2020), and nitrogen fixation capacity of the microbiome was found to vary significantly by water depth within Antarctic benthic mats (Dillon et al 2020). pH levels were found to influence the microbiomes of Icelandic cold springs  (Guðmundsdóttir et al 2019) and Mangrove-associated waters (Dhal et al 2020); and the archaeal composition of Beijing urban lake sediment (Wang et al 2020). 

Water-associated microbiomes are dynamic across gradients, geography and time

While water bodies exhibit heterogeneous physiochemical and nutrient properties depending on their environmental and geographical circumstances, the articles in this collection demonstrate that many water-associated microbiomes fluctuate predictably and periodically. For example, the diversity of seawater microbiomes exhibited diel fluctuation, which itself was characterized by rhythmic changes in temperature and concentrations of nitrate, ammonium, phosphate and silicate (Weber et al 2020). Microbiome structure and composition also correlated with gradients established by water depth (Dillon et al 2020, Weber et al 2020), eutrophication (Dhal et al 2020), and distance from coral reefs (Weber et al 2020). These findings emphasize the importance of the physical environment from which water samples are collected, and the fact that water and water-associated samples are inherently connected to — and impacted by — features that may be located far away from the actual sampling site. This highlights the importance of contextualizing sampling sites both temporally and spatially.

Featured papers, which can be found here.

  • Paltu Kumar Dhal et al, Insights on aquatic microbiome of the Indian Sundarbans mangrove areas
  • Megan L. Dillon et al, Environmental control on the distribution of metabolic strategies of benthic microbial mats in Lake Fryxell, Antarctica
  • Ragnhildur Guðmundsdóttir et al, Bacterial diversity in Icelandic cold spring sources and in relation to the groundwater amphipod Crangonyx islandicus
  • Yuxin Wang et al, Comparative Study on Archaeal Diversity in the Sediments of Two Urban Landscape Water Bodies
  • Amy Apprill et al, Diel, daily, and spatial variation of coral reef seawater microbial communities
  • Robert Hilderbrand et al, Using the microbiome to assess the ecological condition of headwater streams

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.
A picture pointing downwards at two hands wearing gardening gloves and holding handfuls of soil in each hand. Roots and leaves protrude from the soil and the grass on the ground is blurred in the background.

Compost, food security, and social justice

What do compost, food security, and social justice have in common? They are all part of creating sustainable, more localized food systems that benefit the community. Want to know more? Check out the piece I co-wrote for The Conversation, along with two other soil microbe researchers.

City compost programs turn garbage into ‘black gold’ that boosts food security and social justice.” Kristen DeAngelis, Gwynne Mhuireach, Sue Ishaq, The Conversation. June 11, 2020

Dr. Kristen DeAngelis is an Associate Professor who studies microbes in soils, climate change, and human impacts, and Dr. Gwynne Mhuireach, a post-doctoral researcher who studies microbes in soils in the built environment and human health.

Woman dressed in a costume of a dissected cat, to teach a class on Halloween.

Teaching students to give scientific presentations

This semester at UMaine, I’m teaching a section of AVS633/FSN671 Graduate Seminar, for students in the Animal and Veterinary Science and the Food Science and Nutrition grad programs. Naturally, I decided to spice up the course requirements.

In all the presentations I have given; during classes, teaching, as public lectures, guest seminars, and conference proceedings, I’ve faced a great deal of technical and audience-related challenges. There is a wealth of information on the formatting and content aspects of building a scientific presentation, but in my experience, that’s only half the battle. The other half is in being able to accurately and interestingly relay that information to your audience. Even in professional settings, I have faced disruptive technical failures that caused me to alter my talk or have to adjust my narrative, and I have fielded poorly-crafted or poorly-intended questions from my audience, all while trying to maintain my composure.

I felt that this was what the graduate students needed to learn, and in a safe space where it was OK to simply, well, give a bad presentation. To convey this, I put together an introduction to the class (below) and a series of assignments.

The Elevator Speech

Their very first assignment was to stand up, with notes but no slides, and give a 3 minute speech on a topic of their choice. It had to be non-technical, and designed to provide information in an approachable way such that the person stuck on the elevator with you would actually want to hear more. As academics, especially when you are a student, you often get caught up in repeating jargon or with having to explain yourself in highly detailed language to faculty who are training and testing you. You forget how to present your work to someone who has absolutely no background, and only a few minutes worth of attention span to devote to hearing about your very niche research question. To give an effective elevator speech, the students needed to distill only the critical information for someone to follow their line of thinking, and to not get bogged down by extraneous detail.

Peer Presentations and Awkward Audience Questions

For the second assignment of the course, each student was required to give a presentation on their research, their program of study, or a specific topic they were interested in and the relevant research. Due to the number of students and course time allotted, this presentation only needed to be 10 minutes long, but I’ve found it can be more difficult to present your material concisely. The students presented as if to a peer audience, so they could use a certain amount of jargon or introduce methods with minimal explanation. This style of presentation is common in graduate school, and as expected, the students all did incredibly well.

To add a challenge here, I instead focused on the audience (in this case, the rest of the class). The thing about being an audience member that most people never think about, is that you also need to conduct yourself with a certain level of professionalism. It might not be polite to shout a question or snarky response in the middle of a presentation, your comments might seem complementary but are in fact back-handed, or your question might simply be poorly crafted. I have been asked, or been witness to, a lot of poorly-worded audience questions and responses, and I’m not referring to general public audiences, I’m talking about academics who should know better.

To that end, for each student presentation, I gave an index card to another student in the audience to ask or perform during the talk. Participation was voluntary. Some of these are well-meant questions that are simply commonly asked. Others are silly, and some are rude. I didn’t include anything offensive or abusive, but those examples abound. The list is pretty funny, but please, NEVER DO THESE AS A REAL AUDIENCE MEMBER.

  • Ask the speaker if they will be a medical doctor (or veterinarian) after they finish this [research] degree.
  • State that you have a question. Then pose a statement/comment that is not a question.
  • Be on your phone (texting) or overtly not paying attention to the entire presentation.
  • Ask them to explain a simple concept that they covered in their presentation (but that you missed because you weren’t paying attention).
  • Cough or sneeze comically loud, or drop something during the presentation.
  • Ask the speaker how they chose this topic or how they got into this type of research/work. (This seems benign, but can take away from more specific questions during a peer presentation.)
  • Ask if the speaker is familiar with a field/event/discovery that is somewhat related to their presentation but not actually in their presentation.  Example, speaker presents about infectious disease in cattle and you ask them about “cow farts and global warming”.
  • Comment that the speaker looks really young for someone in their position.  Example: “Wow, I thought you were an undergrad! You look really young. I mean, that’s a compliment.”
  • Get up during the presentation and adjust the lights or shades in the room. You don’t have to make them better, just change them.
  • Ask the speaker a multiple part question. They can be simple questions, but ask them all in one, long, run-on sentence.
  • Begin your question with “As a parent,….” even if you are not a parent and the question has nothing to do with being a parent. 
  • Ask the presenter who analyzed their data for them (even if they have already said they analyzed it themselves).
  • Tell the speaker that their method is not valid (but don’t explain why).
  • Tell the speaker: “This was a pretty good presentation. When you have been in grad school a few more years I think you’ll be a really good speaker.”
  • Tell the speaker that this kind of work has been done before and ask what they have done that is unique.
  • Raise your hand to ask a question, but then sit back, squint your eyes, exhale loudly, pause for a moment, then say, “Never mind”.

The Technical Challenge

On multiple occasions, I have had to give a short (10 min) presentation by memory because the slideshow wouldn’t open or advance. I have had poor lighting, or poor color contrasting from the projector, which made it difficult to read my slides. I have had projection screens which were much smaller than I anticipated such that my text was too small to read on figures, and I’ve more or less given up the hope that I will routinely encounter “presenter mode” when using podiums or other people’s machines. I’ve had a projector that kept shorting out during the talk and creating blank screens for 10 seconds, something which you can hear me talk about in the lecture recording but not see on the recorded slides. I’ve had my available time cut in half, had to cut my presentation short because I included too much detail, realized I had poorly organized the presentation of material or forgotten to define a critical aspect, been unable to play videos or animations, had hand-held slide advancers with low batteries, had automatic slide advance turned on by mistake, and more.

When you face these surprises during a talk, you often don’t have the time, never mind the presence of mind, to resolve the problem. You simply have to make the best of it before your time runs out. It helps to know your material, but it also helps to be able to improvise, which is a skill best developed in practice. You might need to fill air time, or reconstruct your presentation on the fly, or make light of the situation to cut the tension in the room. To help my students prepare, I asked them to send me their peer presentation, as I wanted them to use a presentation they had just given and were familiar with. Then, I introduced mistakes into the presentation without disclosing what those might be, only that they would be there.

To think up enough technical problems I could use, I enlisted the help of scientists on twitter. Click on the Tweet below to find the thread and see the other contributions from @HannahMLachance, @canda007, @Wymelenberg, @vaughan_soil, @murphyc1928, @cskrzy, @maria_turfdr, @mcd_611.

I came up with this non-exhaustive list:

  • Replace a video with a still shot
  • Have 2 students make slides on the same topic, then have them present the other one’s slides (to simulate when a co-author gives you some slides on their contribution and you forget what they mean).
  • Reorder some of the slides
  • Remove a lot of the text on the slide
  • Resize images to be too small for audience to see resolution
  • Introduce blank slides to simulate projector connection issues (like screen flickering on/off occasionally)
  • Ppt won’t open at all or won’t advance beyond title slide
  • Change font on all text to tight cursive
  • No ‘presenter mode’ available
  • Resize slide dimensions and don’t adjust proportions to ensure fit
  • Turn laptop around so can’t see screen as if presenting at a podium
  • Add animations to everything
  • Add notification of email on timer (created a shape with animated pop in and out, as well as notification chime).
  • No photos
  • Slide advancer with poor quality batteries
  • Automatic slide advance

Public Presentations

Public presentations are an overlooked part of academia, but a crucial aspect. If you are at a public university, or you receive state or federal funding, your work is being supported by tax dollars. Many federal grants require an outreach or public education portion to your project, where you make the results available to interested parties (called stakeholders). Science communication is also extremely important in bridging the divide between scientific and public communities.

Public presentations need to present information approach-ably. I don’t mean they need to talk down to people, I mean they need to consider that the audience might not have a frame of reference for what you are talking about. I have a PhD, but it’s meaningless if I attend technical lectures on physics. For the third challenge in class, students can give their presentation again but with the knowledge that they can’t throw 20 slides worth of dense information at their audience, they can’t use technical language without defining it, and that sometimes the best way to explain complicated information is using pictures or analogies.

Update: In light of Corvid-19 concerns, campuses have been closing and switching over to remote instruction. This was rather challenging to do well with a presentations class, as giving a webinar isn’t the same as giving a public presentation. To be more creative, I am having students submit their public presentation slides online. I then assign them to another student, who has to annotate the ‘presenter notes’ with the speech of how they would present these slides. I then return the annotated version to the original presenter so they can see how well their slides spoke for themselves. In this “presentation telephone game”, I hope they will see how easy their slides were translatable to someone else, which is a common problem in slides put online without any notes or audio: so much gets lost when the presenter isn’t providing the information and filling in the additional information that is only briefly noted on the slides.

Learning (to Pretend) to Enjoy Giving Presentation

You can’t always control the technical aspects of your talk, or select your audience, or even be prepared for the weather that day. You won’t always be well-rested, or in good health, on the day of. Fun fact about stress, it can trigger spotting or early menstruation. There’s nothing quite as terrifying as being in the middle of your presentation when you are suddenly aware that you have a limited amount of time to get off stage and hope that there are feminine products available for free in the nearest restroom, because your women’s dress pants don’t have pockets for you to carry quarters for the dispensary machines.

You won’t always have time to prepare. Once, I had 5 minutes of notification that I would have to stand up in front of 50 – 75 other college students and Jane Goodall and present a recap on a service-learning course, at a time when I dreaded any and all public speaking. But you can’t really decline the offer to talk in front of Jane Goodall when she had taken the time and effort to be in the room to listen to you all. So you just have to stand up and start talking before you convince yourself you can’t do it.

You can have faith in yourself, know that you will try your best, and remind yourself that it will be good enough. I’ve been an audience member at perfect presentations, and I remember that it went really well and nothing at all about the content. The talks that I remember most are the ones where the speaker connected with me. They were funny, they were humanizing, and they took technical problems and awkward interactions in stride.

The best way to become a better speaker, I think, is to be open to the idea that you are going to mess up. A lot. But each time, you will learn from that experience, you will ask for feedback, and you get back out there. As academics, we have to present information on nearly a daily basis. It is, in fact, a significant part of the job. So instead of dreading it, we should at least pretend to enjoy it until, one day, we find that we do.