Last week, I gave a presentation to the University of Maine Cooperative Extension Oxford County 4-H Jamboree.
The video is available on YouTube, with subtitles! I sat down to learn how to create and embed them in videos, to help make my science more approachable. The video is made for kids and contains suitable content for all ages, although the difficulty of the content makes it best for kids 12 and up.
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.
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.
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.
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!
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:
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.
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.
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.
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.
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.
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.
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.
Looking for kids’ activities for the summer? Check out the virtual programs hosted by the University of Maine Extension 4H! Learn about animals, how to care for them, and how your food system works.
From their main page, you can find descriptions of each virtual session, including subject material, presenter, and recommended age group (k-12). You can register for as many or as few sessions as you like, which will be delivered over Zoom.
Registration is free! But if you are able to donate to support the program, those are welcome through the 4H site.
I’ll be presenting on Thursday, August 13th, 2020 at 3 pm EST.
Learn about different digestive tracts in livestock, and the community of microbes living there that help animals digest food, or stay healthy. This presentation will give some background on different digestive tract anatomy, the factors which influence microbes in the gut, and how we can care for animals by caring for their microbes. This presentation will also feature a short presentation on Dr. Ishaq’s journey into science and a Q&A session where attendees can ask questions about gut microbes, life as a scientist, or how to get involved in this time of career. Register by August 12.
Youth ages 12 & up; open to all youth.
In a 2019 collaboration between the Biology and the Built Environment Center at the University of Oregon and the Oregon Health & Sciences University, we sampled various window surfaces from patient rooms in a hospital ward. We characterized the viable bacterial community located on these surfaces, and investigated the association of relative light exposure of the surface (in direct light or not), the cardinal direction of the room (and roughly the amount of total light exposure in a day), and proximity of the patient room to the nurses’ station (which has higher occupancy and traffic).
The microbial community found in buildings is primarily a reflection of the occupants, and in the case of hospitals, the microbiota may be sourced from patients, staff, or visitors. In addition to leaving microbiota behind, occupants may pick up microorganisms from building surfaces. Most of the time, this continuous exchange of microorganisms between a person and their surroundings is unremarkable and does not raise concerns. But in a hospital setting with immunocompromised patients, these microbial reservoirs may pose a risk. Window glass, sills, and the surfaces around windows are often forgotten during hospital disinfection protocols, and the microbial communities found there have not previously been examined.
This paper is the first first-authored research paper from a former undergraduate mentee of mine at the University of Oregon; Patrick Horve.
Horve, P.F., Dietz, L., Ishaq, S.L., Kline, J., Fretz, M., Van Den Wymelenberg, K. 2020. Viable bacterial communities on hospital window components in patient rooms. PeerJ 8: e9580. Impact 2.353. Article.
I’m pleased to announce that an article was published today on soil microbes, climate change, and agriculture! As local climates continue to shift, the dynamics of above- and below-ground associated bio-diversity will also shift, which will impact food production and the need for more sustainable practices.
This publication is part of a series, from data collected from a long-term farming experiment in Bozeman, MT, led by researchers at Montana State University with whom I have published several times, including:
In this study, cropping system (such as organic or conventional), soil temperature, soil moisture, the diversity and biomass of weed communities, and treatment with Wheat streak mosaic virus were compared as related to the bacterial community in the soil associated with wheat plant roots.
This paper is open-access, which means anyone can read the full paper.
Ishaq, S.L., Seipel, T., Yeoman, C.J., Menalled, F.D. 2020. mSphere DOI: 10.1128/mSphere.00340-20. Article.
Little knowledge exists on how soil bacteria in agricultural settings are impacted by management practices and environmental conditions under current and predicted climate scenarios. We assessed the impact of soil moisture, soil temperature, weed communities, and disease status on soil bacterial communities between three cropping systems: conventional no-till (CNT) utilizing synthetic pesticides and herbicides, 2) USDA-certified tilled organic (OT), and 3) USDA-certified organic with sheep grazing (OG). Sampling date within the growing season, and associated soil temperature and moisture, exerted the greatest effect on bacterial communities, followed by cropping system, Wheat streak mosaic virus (WSMV) infection status, and weed community. Soil temperature was negatively correlated with bacterial richness and evenness, while soil moisture was positively correlated with bacterial richness and evenness. Soil temperature and soil moisture independently altered soil bacterial community similarity between treatments. Inoculation of wheat with WSMV altered the associated soil bacteria, and there were interactions between disease status and cropping system, sampling date, and climate conditions, indicating the effect of multiple stressors on bacterial communities in soil. . In May and July, cropping system altered the effect of climate change on the bacterial community composition in hotter, and hotter and drier conditions as compared to ambient conditions, in samples not treated with WSMV. Overall, this study indicates that predicted climate modifications as well as biological stressors play a fundamental role in the impact of cropping systems on soil bacterial communities.
Congratulations to all three University of Maine undergrads in the Ishaq Lab for making the Dean’s List in Spring 2020: Jade Chin (AVS), Nicholas Hershbine (EES), and Emily Pierce (AVS)!!
Note, the Bowdoin Dean’s List is announced annually in the fall.
Summer 2020 is…. here. This year has been unpredictable at best, but some things have stayed the same. For example, summer is one of my favorite seasons in which to work in science, because things calm down when the university is not in full session and I’m not facing a deluge of emails, meetings, and myriad small interactions that accumulate to eat up the day. I’ve been taking the time to prepare my laboratory, dive deep into scientific writing, and prepare for the increased teaching load I will have starting this fall.
You might think that the pandemic causing months of delayed or reduced labwork would have lightened my research load, but I’ve had more than enough to keep me occupied over this spring. Not only have I been submitting a few manuscripts for peer review at scientific journals from my time at the University of Oregon and Montana State University, but I have been working on some unanticipated manuscripts that coalesced this spring. This has included a project with a previous collaborator on diet and health, another based on soil microbial ecology led by master’s student Tindall Ouverson at MSU, and three more which were generated during my DNA sequence data analysis course that I taught this spring! Of these, I am lead author on two and contributing to the others at a variety of depths. Some require a great deal of my time, while others require only editing and review.
And then there were 10! I now have three University of Maine master’s students and 4 undergraduate students performing research in my lab, as well as three other graduate students from other labs who are affiliated with us (as in, I am on their committee). In addition to training them on scientific research theory, laboratory protocols, and data management and analysis, they are getting general training in scientific literature review and critique, scientific writing and presentation, and laboratory management.
I am preparing the second of two laboratory spaces for my research, and this space hasn’t been fully renovated in years. While still very functional, there have been a number of remodeling, refinishing, and reorganization steps which needed to be taken to get it in line for biosafety level II microbiology work.
I have been doing much of this work personally, because it’s cheaper, and I have experience in basic home renovations. And, I enjoy the opportunity to put my email inbox away and let my thoughts wander to scientific theory while I use power tools.
When it is ready, I’ll be starting the wet-lab research into gut microbiology and doing more culture work to supplement the genomics work. To aid in that research, I’ve been acquiring more nifty bits of equipment.
Over the spring, I piloted a new course as a special topics version, and I have just been approved to teach that as an official course starting in spring 2021! This summer, I have and will continue to revise my teaching materials from the spring version to prepare them for AVS 454-554 next year.
I’ll be teaching two courses starting in fall 2020, one on animal microbiomes and one on undergraduate research for animal science students. AVS 254, on animal microbiomes, is material I have taught at other institutions with a different course focus. For that course, I will be updating the course material, adding new lectures from scratch, and revising the formatting of powerpoints. I’ll also need to make some of it more accessible for asynchronous online learning, depending on how the semester is organized this fall. This means pre-recording the lectures, and putting more effort into the online learning software I have available.
The other course I am teaching is new to me, AVS 401 (and 402 each spring), the AVS Capstone experience. I’ll be teaching students how to write scientific proposals, research papers, and give scientific presentations, as well as guiding them through participation in research along with faculty mentors. For many students, it’ll be their first experience participating in research. This year, since many students are unable to participate in in-person research and labs have been closed, it’ll be extra challenging to come up with projects, but I have some creative ideas in mind.
In addition the above objectives, I have a number of things in development which are not yet ready to be shared in detail. These includes new research collaborations, leading a team to organize a journal special collection, and leading a team to organize and host a (virtual) mini conference meeting in the fall!
Now, as an assistant professor at the University of Maine, I’m on a 9-month contract. During the academic year, I devote 50% of my time to research-related activities, and 50% to teaching/advising/mentoring– related activities. I have the option of working in the summer, or taking it off unpaid. However, my summer salary is contingent on me being awarded research funds which will pay for the work, something which is not guaranteed in this funding climate. It is generally not advisable for pre-tenure faculty to spend summers idle, and in any case, I would inevitably have to perform work of some kind over the summer to keep pace with my workload.
I am lucky enough to have start-up funding which can pay up to 2 months of summer salary per year during my first 3 years; however, I am expensive: one month of my summer salary is the equivalent of 1 full-time undergraduate researcher for 3 months, or a sizable chunk of a research project. On the one hand, I want to value my time and effort, and being paid for summer research helps close the gender pay gap for salary and retirement contributions. On the other hand, I am also forced to consider how to get work done on a reduced budget, should federal funding not come through. After all, being awarded tenure is contingent on productivity.
In May, I was adamant about taking the entire month of July off, as 2019 and 2020 have been incredulously busy and stressful and I haven’t had a vacation since Feb 2019. Now, at the end of June, I’m not sure I could take off a full summer month and still output all of the above, plus be prepared for the challenges of teaching this fall. At least my working-from-home view is more or less a vacation-scape, and some surprise home renovations will at least keep me away from electronic screens for some of it.
Not only is the ongoing ‘COVID-19’ pandemic a collective experience and historical event, it has changed the way we interact with each other and with our infrastructure. It’s pertinent to incorporate these events into teaching curricula, not only to study these changes in real time, but to help us make sense of what is happening during these difficult days. A number of faculty at the University of Maine have been and will be integrating various aspects of the pandemic into their teaching. For my part, I’ll be guiding students on research projects related to how COVID-19 and public policy has affected agriculture and veterinary practice.
“COVID has very suddenly and dramatically changed the way we interact with each other, and has had repercussions for food, agriculture and animal care industries,” Ishaq says. “Students need to understand these changes to build more resilient and sustainable food and health care systems.”
“Faculty incorporate COVID-19 content into curricula”, Marcus Wolf, June 23, 2020
Featured Image Credit: Miriam Webster
A second course that I developed was accepted at the University of Maine! AVS 454-554 DNA Sequencing Data Analysis will be offered to undergraduate and graduate students starting Spring 2021.
AVS 454-554 teaches bioinformatics using DNA data. Starting with raw DNA sequencing data, students go through the process of quality assurance, statistical analysis, graphics design, as well as drafting a scientific manuscript. The course integrates research into teaching by using unpublished data, ideally data the students bring from their own research projects. Not only do students learn highly sought-after analytical and scientific writing skills, but it makes them active participants in research and their own learning. Most of the course time and skillset are focused on amplicon sequencing data, but we’ll also dabble with whole-genome, metagenomics, and metatranscriptomics.
Along with my Introduction to Animal Microbiomes course, I hope to get students interested in microbial ecology earlier in their studies, such that they have time to get involved with microbial ecology research in Maine in time for them to develop a Capstone research experience around it in their senior year. And what a coincidence, I’ll be teaching the Capstone courses for AVS (401 and 402) starting in fall 2020, as well.
This course is based on the precursor version, AVS 590, which I taught as a small, special topics version in the 2020 spring semester. And, even that is conceptually based on a lab section I taught at Montana State University in 2015 and 2016. DNA data analysis and I go way back.
It can take several months to get course proposals approved, especially if you are proposing they meet general education requirements, are listed as required for a major degree, or have other levels to them. I started Sept 1, and the AVS faculty curriculum committee, the first step in the approval process, was meeting in early October. I didn’t have time to develop two course proposals in time, so I first proposed my data analysis course as a “special topics” version. These versions are offered selectively and are not counted the same way as an approved course. But, it gave me time to shore up my teaching materials, and teach several students who were graduating and couldn’t wait another year to learn these skills.
DNA sequencing data analysis is challenging to teach as well as to learn, but once over the learning curve, it can be extremely fun and rewarding. I’ve previously taught bioinformatics to undergraduates, and have or continue to publish with a number of them. In AVS 590 in the 2020 semester, there were 4 datasets being analyzed, and 3 of those led to manuscripts which are anticipated to be submitted to for review in scientific journals sometime this year!
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.
The Ishaq Lab 