Rumening through camel microbes, by Myra Arshad

Written by Myra Arshad

Myra Arshad

Did you know that camels have three stomach chambers or that they have to throw up their own food in order to digest their food properly? Have you felt excluded from science spaces before? Then this blog post is for you!

Allow me to introduce myself. 

My name is Myra, and I am a rising senior at SUNY Stony Brook University, where my major is Ecosystems and Human Impact, with a biology minor. In a nutshell, my major is interdisciplinary with a focus on conservation and ecology within human societies. 

If I were to describe my college experience in one word I’d pick “surprises”. I never actually saw myself being a scientist in my middle and high school years. I found it hard to care about abstract concepts or theories that felt so far removed from humanity, particularly minority communities. But, during college I found myself falling in love with environmental studies, and along with it, the beautiful complexities that come with being human in our increasingly anthropogenic world. 

At UMaine, we focus on the One Health Initiative, which views the health of humans, animals, and the environment as interconnected. When COVID-19 caused everyone to go into lockdown, I was fortunate to find this farm was looking for crew members, with a focus on food security. While certainly not how I planned to spend the summer of 2020, farming for underserved communities is where I saw how impactful One Health was. Organic farmers commonly use plastic mulch as a popular alternative to pesticides for weed suppression. At my home institution, I lead a project on the impacts of microplastics on earthworm health, an Ecotoxicology lab (students of the lab affectionately gave it the nickname “the Worm lab”).  We use earthworm health as an indicator of soil health, which in turn is crucial for crop flourishment. The Worm Lab and farming emboldened me to pursue science and, ergo, look for this REU! 

At UMaine, I am a member of the Ishaq Lab where I work on the camel metagenome project. Basically, scientists in Egypt raised camels on different diets, then used samples from their feces to sequence their microbial genome. These microbes live in the camel rumen (part of the camel stomach), and help the camel digest their food. What I do with Dr. Ishaq’s lab is, I perform data analysis on these sequences to see how the microbial gene profile changes with different diets. Camels are essential for transportation and food for the communities that rely on them, so finding the most efficient feed for them is important. Camels also release methane depending on their diet so it’s possible humans could control methane production of camels through their diet. 

Being a part of the REU ANEW program for 2021 definitely has been an interesting experience, since it is the first time this program has been conducted virtually. Even though I would have loved to have seen everyone in person and spent time in lovely Orono, Maine, I’m glad for the research opportunity as it has further solidified my love of research and the One Health initiative.

Myra’s poster for the REU Research Symposium, virtual, Aug 13, 2021.

Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice

The Microbes and Social Equity Working Group is delighted to make its published debut, with this collaboratively-written perspective piece introducing ourselves and our goals. You can read about us here.

This piece also debuts the special series we are curating in partnership with the scientific journal mSystems; “Special Series: Social Equity as a Means of Resolving Disparities in Microbial Exposure“. Over the next few months to a year, we will be adding additional peer-reviewed, cutting edge research, review, concept, and perspective pieces from researchers around the globe on a myriad of topics which center around social inequity and microbial exposures.

Ishaq, S.L., Parada, F.J., Wolf, P.G., Bonilla, C.Y., Carney, M.A., Benezra, A., Wissel, E., Friedman, M., DeAngelis, K.M., Robinson, J.M., Fahimipour, A.K., Manus, M.B., Grieneisen, L., Dietz, L.G., Pathak, A., Chauhan, A., Kuthyar, S., Stewart, J.D., Dasari, M.R., Nonnamaker, E., Choudoir, M., Horve, P.F., Zimmerman, N.B., Kozik, A.J., Darling, K.W., Romero-Olivares, A.L., Hariharan, J., Farmer, N., Maki, K.A., Collier, J.L., O’Doherty, K., Letourneau, J., Kline, J., Moses, P.L., Morar, N. 2021. Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice. mSystems 6:4.

Responsible conduct of research – oversight, training, and more

One aspect of research which requires substantial training, adherence, and reflection for researchers, yet gets almost no public attention, is the rules and regulations on the responsible conduct of research. In this piece I focus on the US, but many countries have ethical guidelines of their own. This piece is meant as a reflection of how far science and society have come, and while ethics in science are only as good as the scientist, I wanted to share the stringent approval and review processes that modern research must go through prior to completing any work, to ensure safety and respect for all persons and animals. Thus, please don’t read the first section and run off thinking that researchers are monsters – it is there to give you an understanding of where we ae now.

Bias and the misuse of research

If you’ve ever read “The immortal life of Henrietta Lacks”, by Rebecca Skloot, you are familiar with a high -profile case which took decades to uncover. The book examines the case of a woman, Henrietta Lacks, with cervical cancer whose cells have revolutionized medicine and research.  However, doctors didn’t ask for her permission to use those cancer cells, she didn’t know they were being taken, her family didn’t know they were being used extensively in research labs around the globe, and even decades later they have not benefited from the billions of dollars of research and development profits that came about because of her cells.

History is littered with examples of cruel or nonconsensual research going back hundreds of years. Most of those involve intensive research on humans or animals without their knowledge or their consent, other examples include disregard for safety or privacy. Even decisions which appear benign but are still unethical prevent people from benefitting from their own contributions to research.  

However, nearly all of these historical examples involving human subjects research are rooted in racism, sexism, and/or anti-religious or religion/ethnic cleansing. Historically and today, science has often been intentionally misconstrued to perpetuate social constructs of superiority/inferiority. Science is only a tool, and while these examples can be blamed on individuals choosing science to be the tool of their ill-intent, the historical lack of ethical guidelines, constraints, or consequences belies the failure of society to ensure equality and respect to all persons. There are numerous resources (for example, here and here) which examine these past offenses in detail, and reflect on how they led to the ethical guidelines we have in place today. 

In addition to the obvious harm it could cause, not incorporating ethics into research contributes to Institutional Betrayal.  This concept was coined by psychologist Dr. Jennifer Freyd, and describes the harm caused or allowed to happen by an institution, which causes psychological damage because you expect the institution to protect you. Collectively, unethical research leads to a distrust of science, researchers, and medical professionals, and can lead to science denialism.

One of the challenges to understanding ethics in scientific research is that our ethics reflect our values as a society and those values and laws change over time.  You only have to read the news to see that we all have different ideas about what is acceptable to do to someone else.  We should not think of everything that is permissible as also acceptable: just because you can do something, doesn’t mean you should do it. And, you can still take advantage of someone even if you are not physically harming them. Thus, ethical standards inform what we are able to research, but also why we are doing it, and how, as there may be less invasive methods available.

Importantly, ethical standards takes power away from the researcher and puts it into more objective hands. If a researcher wants to do a project, and millions of dollars of research funding, 20 research staff, and their careers are all based on the research succeeding, that puts a lot of bias in all of their thoughts and actions.  Ethical review helps ensure that researchers are making good decisions before, during, and after the research.

Perception of authority and power dynamics

Americans have historically distrusted science, and this has always been encouraged by various social and political entities. This external influence on our perception of science has intensified in recent years, which has become dramatically clear in the way that people have responded to the pandemic. However, generally when people look at photos of researchers, scientists, or doctors, and they respond that they have some level of trust in them. This trust, of course, varies by gender and race and is rooted in how certain demographics have been taken advantage of previously.

There is a term called perception of authority, which can be used to describe how people ascribe authority to researchers, scientists, and doctors simply based on visual cues (like wearing a white coat). However, this perception can be incorrectly attributed to people who appear to be in that same category but are in fact not trustworthy or knowledgeable about the topics they claim to be experts in, for example, some TV personalities

Ethical standards and review prevent researchers from intentionally or unintentionally taking advantage of participants’ willingness to say “yes” based on their perception of you being an authority, whether or not you really are. That is just one example of a power dynamic.

Research sets up a power dynamic, which is a relationship wherein one person has more power, authority, or control over another person. In research, there are a lot of ways in which that can be set up.

In addition to perception of authority, there is a perception of luck, in which participants assume they will be in the placebo group (the control group which receives no treatment to make sure the effects you see are because of the treatment and not just from the excitement of being in a research study) and dismiss concerns about potential risks. Financial incentive for participating may recruit people that really need that money and feel pressured to be int he study regardless of the risks. There is also the hope of a cure. For medical research involving obscure or rare diseases, studies may use developmental treatments and by necessity must recruit participants who suffer from this particular problem. You might be more like to participate if you assume that the treatment will cure you, or if you don’t understand that it is equally likely that you could be in a placebo group as in the treatment group. There are also people that feel pressured to consent because they have less social impact and power and feel that they can’t say ‘no’ to participation, by refusing to enroll or by withdrawing from the study at any time. Ethical regulations specifically include prisoners, children, pregnant people, and anyone without the ability to make an informed decision under special protections against power dynamics, but ethical review boards will help you identify other situations or demographics and how to lessen those power differentials.

In addition, having a study approval that rests with a committee who are in no way involved with the research can help reduce bias or harm. These standards may require researchers to be more creative in order to do less harm and find a better way to conduct that research, either by using alternative methods or fewer participants. Ethical review boards also ensure that researchers get the most out of the study, such that if some harm, even just some inconvenience, is being done to someone (human or animal), the benefits from the study are worth the cost and that judgment call is made by someone with no stake in the research. Review also ensures that the study is designed to collect as much info as possible so that it does not have be repeated.

Ethical standards also require researchers to obtain informed consent from your human participants. This includes what will be done to them during the study, what information or samples will be collected, what information (including methods) will be obtained from these samples, and what will be done with their samples or information in the future. Finally, ethical standards creates accountability for researchers’ actions by creating a paper trail, setting up oversight on the project, and creating consequences for failure to comply with regulations.

The logistics of ethics

How do we add ethical principles to our research?  To summarize, you want to minimize harm to participants, be transparent about your activities and keep human participants well informed, keep excellent records and document all communications and information you share with human participants, always get Institutional approval before conducting research or collecting samples or information, and try to reduce the power dynamic by making yourself accountable for your actions. There are many guiding principles available, including some listed here provided by the NIH:

  • Social and clinical value
  • Scientific validity
  • Fair subject selection
  • Favorable risk-benefit ratio
  • Independent review
  • Informed consent
  • Respect for potential and enrolled subjects

Institutional Animal Care and Use Committees (IACUCs)

If research involves live, vertebrate animals in some way and has a hands-on or disruptive aspect, approval from the Institutional Animal Care and Use Committee (IACUC) is required prior to starting the work. These regulations and guidelines stem from animal welfare laws and guidelines.

You should always consult with your IACUC board about your project before you have made preparations or started any work, as they should be kept apprised of research for reporting purposes and are the ones to verify if you do or do not need a formal approval. You typically don’t need formal approval if you are only observing animals and not interfering with them in any way or holding them captive, if you are collecting discarded animal products (like feathers), or if you are collecting tissue from carcasses. Keep in mind, you will need institutional biosafety approval to conduct this research if there is a specific infectious disease concern, and you need approval from your state fish and wildlife department if you are collecting samples from wild animals (even more so if the animal has a protected status). If you will be transporting biological material across state or national borders, there is another layer of training and approval before you can begin.

Each institution which performs animal research in the US is required to form at least a 5-member committee, which has to include the attending veterinarian at the institution with experience and training in the care and use of laboratory (and livestock) animals, one member from the local community, a practicing scientist experienced in research involving animals, a non-scientist, and at least one more member of any kind (usually another practicing scientist at the university). 

In addition to applying to IACUC for approval for your study, you’ll need to document that everyone on the project has completed relevant training on responsible research conduct, animal handling, and the procedures you will be using. Some of that training is administered by your institution, but much of it will be performed through the Collaborative Institutional Training Initiative (CITI), which provides standardized information and training.

Institutional Review Boards (IRBs)

If research involves humans in some way, including surveys, approval is required from the Institutional Review Board (IRB) prior to starting the work.  Even if your project ultimately does not require approval, you should always contact your IRB first, to let them know what you intend, and get their informal approval that you don’t need formal approval from the committee to do your work.

The members of the IRB committee may not have a personal, professional, or financial conflict of interest, and the federal code of regulations stipulates many guidelines about membership:

“Each IRB shall have at least five members, with varying backgrounds to promote complete and adequate review of research activities commonly conducted by the institution. The IRB shall be sufficiently qualified through the experience and expertise of its members, and the diversity of the members, including consideration of race, gender, cultural backgrounds, and sensitivity to such issues as community attitudes, to promote respect for its advice and counsel in safeguarding the rights and welfare of human subjects. In addition to possessing the professional competence necessary to review the specific research activities, the IRB shall be able to ascertain the acceptability of proposed research in terms of institutional commitments and regulations, applicable law, and standards of professional conduct and practice. * * * The IRB shall therefore include persons knowledgeable in these areas. If an IRB regularly reviews research that involves a vulnerable category of subjects, such as children, prisoners, pregnant women, or handicapped or mentally disabled persons, consideration shall be given to the inclusion of one or more individuals who are knowledgeable about and experienced in working with those subjects.”

Code of Federal Regulations, Title 21, Volume 1, Revised as of April 1, 2020, CITE: 21CFR56.107

Generally speaking, you’ll need IRB approval (and training) if you intend to publish this work or share this information widely, if you are collecting sensitive information (such as health, finances, or anything which would put the safety and wellbeing of that person at risk if it were revealed), if you are collecting (biological) samples, if you are doing anything physically or psychologically invasive, or if you are working with vulnerable populations. If you will be transporting biological material across state or national borders, there is another layer of training and approval before you can begin.

There are a number of information-gathering activities that don’t require review and approval, most of which are student projects that are part of coursework. These include interviewing one person for a biography on non-sensitive information, or interviewing multiple people on non-sensitive topics (such as asking about their favorite animal), performing a literature review or information search on non-sensitive or de-identified information, or creating science curricula.

Biosafety and chemical regulations

In addition to regulations on working with biological study subjects, there are additional health and safety regulations if your work involves anything infectious or dangerous. Institutional biosafety and chemical safety review requires researchers to describe all protocols, sample types and relative risks, and all safety and containment procedures – from the protective gear you will wear, to your sterilization or detoxification procedures, to the equipment you are using that could cause aerosolization and spread. There are yearly chemical and biosafety inventory reviews, laboratory walk-through audits, training, reporting, and equipment maintenance records that all go along with this.

Consequences

Like any good policy, responsible research is best accomplished when there are consequences and an institutional dedication to enforcement. Not only are applications and training required prior to performing the research, but there are facilities audits, reporting, and other regular check ins. Because there is no much to keep track of, review boards and enforcement are there to help researchers set up good practices and protocols ahead of time, help you stay in compliance, and correct problems before they exacerbate. Researchers who refuse to obtain permission prior to sample collection, who change their protocols without notifying review boards, who flaunt regulations, or who commit ethics violations will risk losing their funding, their job, and in severe cases, could face criminal investigations.

A brief history of the brief history of academic tenure

If you are in academia, you probably hear the word “tenure” at least once a week. It seems like an entrenched policy, but you might be surprised at how relatively new this feature is. When I speak to people outside of academia, usually people are surprised to hear that I am facing yet another hurdle even after I got a faculty job. I thought I would summarize tenure, but will mostly point to other resources which reflect on this in more detail. I’m focusing on US higher education as I’m most familiar with those nuances, though higher education in other countries and/or research institutions around the globe also use tenure.

Tenure is a permanent and guaranteed contract (in academia). While it was initially used as early as the 1600s, it wasn’t until the 1900s with missives from the Committee on Academic Freedom and Academic Tenure of the American Association of University Professors that formal policies and legislation began to pop up. The impetus behind tenure is to support academic freedom: to protect researchers from being fired for political or social retaliation, or because their work is less exciting than other topics. The pursuit of knowledge is inherently tied to social and political contexts, and certain topics are considered unimportant by people who don’t work in that field, but research directions should not be determined by opinions.

Once conferred by an institution, tenure can only be terminated for financial or legal malfeasance, or the dissolution of the academic/research program, and can supersede retirement age policies. In some encouraging cases more recently, the tenure was terminated for reasons of patterns of sexual misconduct and perpetuating a hostile work environment.

You must apply for tenure at your institution via an arduous, multi-year process, in which you essentially apply for the job you already have but forever. Not all positions are eligible, and those which are are labelled as “tenure-track”. Once you are hired, your tenure clock begins, with a few checkpoints along the way that vary based on institution and department. You will always have a 3 – 6 member peer-review committee (formally called the Promotion and Tenure Committee), made up of tenured faculty from your department/school who are qualified to assess your work. Committee members are elected to serve in 1 – 3 year shifts by the department. They are supposed to guide you, offer mentorship, and provide feedback. Ideally, you meet with your peer committee annually along your track to improve your tenure application over several years.

There are two major checkpoints, your third year review, and your tenure application review. The third year review is when the peer-review feedback carries more weight. If there is something your committee wants you to correct, you’ll only have a few years to ameliorate it before you formally apply. Most tenure-track positions allow up to 7 years to formally apply for tenure, although this varies and clinical research positions usually have longer. The common time to apply is five to six years after you begin your position, but you may apply sooner (depending on institution deadlines) if you meet the requirements, or “pause your clock” during parental, medical, or other approved care leave.

Your tenure packet is a giant application with reflections on your teaching, research, ability to obtain funding, outreach, and impact in your field. You need to solicit letters of support, but also have reviews from people in your field that you have no ties to. Your application is reviewed by many layers of oversight, which can include but are not limited to: your peer review committee, your department chair, your college/school dean, the provost, and the university president. Each layer of review needs to agree that you should be awarded tenure. For most assistant professors, you are assessed for promotion to associate professor at the same time, but you can be awarded tenure without being awarded a promotion (you’ll meet the peer committee every few years over your career to go apply for promotions or merit adjustments to your contract).

You can apply multiple times, but there is a significant risk associated with it after you have been denied somewhere in the chain at your institution. Typically when you apply in your fifth or six year you can only re-apply once, or challenge a denial once. Denial of tenure can occur because of poor performance, or perceived poor performance if you did not present yourself clearly, but there are also instances of outright discrimination. While your teaching evaluations and record are evaluated, it’s really your research record which counts (including papers published, citations, and grant funding received). In all cases, it can be demoralizing, traumatizing, incredibly disruptive to your career and success, and is costly – the institution put enormous amounts of time, money, and support into tenure-track faculty, and it is immensely more expensive to deny tenure and lose someone than it is to make sure they are actually getting the support and mentorship they need. However, it is not necessarily the end of the road for researchers.

Tenure policies are hotly contested, and many opponents cite that tenure promotes “laziness” despite the demonstrably long hours of faculty and the fact that many of us aren’t necessarily paid for our work during the summer. Faculty on 9-month contracts must obtain funding for their summer salary for research, and if funding sources are tight, you essentially have to work for free to still be productive enough to be deemed worthy of funding in the future. Notably, there is a very distinct relevance to the career level of the tenured person in these pro/con tenure arguments: tenure-track is seen as extremely beneficial in protecting early and mid-career faculty, but protective of unproductive faculty, particularly at or past the age of retirement. Thus, there are many examples of suggested alternative practices which offer protection alongside time limits.

Tenure is not just about offering protection for academic freedom, it also provides a structure for success in research and education. In the past few decades, there has been a dramatic reduction in the number of tenure-track faculty in the US (only ~25% of faculty positions are currently tenure-track), despite the growth of student populations. Instead, this burden has been shouldered by an increase in short-term contracts, because tenured faculty are costly and adjuncts can be dismissed at any time. However, this trend is based purely on cost-savings for institutions, as it can be extremely disruptive to student education because inadequate contracts force adjuncts to work multiple jobs and undercuts their ability to interact with students. And, it can dramatically reduce the quality of life and quality of employment in academia.

Reducing tenured positions also hampers scientific progress and short-contract researchers. Funders can be less willing to reward funding to researchers without a secure job contract. Most importantly, though, it can take years to build the momentum to conduct thorough and cutting-edge research, and long-term contracts allow for better research, and more lab employees trained. Having had to pivot between a series of short-term contracts which ended sooner than expected, I often wonder if the quality and depth of my research would have been dramatically better if I had had a longer-term contract anywhere prior to my position as an assistant professor.

A clock with wings flying in the air, with another one in the background out of focus. The background is a blurry tan.

Reflecting on “suggested deadlines” for assignments

Over the Fall 2020 semester, I changed my assignment deadline policy, creating “suggested deadlines” instead of enforced ones. I altered the language to “suggested deadline” in my syllabus semester timeline (in which I provide due dates for all assignments), I left submission portals open in the online teaching software, and I did not manually penalize grades for lateness. I made the change out of practicality for the fall semester, and I was personally pleased by the results; however, I wanted to hear from students. After being able to formally obtain student feedback during course evaluations, I wanted to reflect on that change and how I will implement it in future courses.

Previously, when grading policies were up to me, I accepted late assignments with a possible -10% grade penalty reduction per day, although I would waive it for a variety of circumstances. It was easy to enforce using online teaching software which timestamped submissions. This policy seemed to motivate some students, but in retrospect, it made students feel like they had to share their reasons for lateness and justify why they needed an extension. Not only did this late assignment policy increase the number of emails I received and time spent replying that yes, I would still accept it, but it also meant that students were sharing more personal information with me. I suspect that students who did not ask for deadline extensions probably had a reason but didn’t want to share than information in asking for an extension, and really, it is none of my business what else is going on in their life.

However, I made the decision to allow any assignments to be turned in after the due date without a penalty, in part because the pandemic shifted the amount and type of work most students were doing. Many of them reported an increased workload, having to attend remote classes in their car, trouble with internet access with so many other users on their network, and of course, power and internet outages are common in Maine when trees topple utility lines. If I had enforced assignment deadlines, then a third to a half of my students were in danger of failing the course because of lack of work, but not because of poor quality of work. This was unreasonable to me, especially in my undergraduate research course where I would be effectively be penalizing students for delays caused by their research mentors or haled research on campus.

So, I made the decision to trust my students to manage their own motivations and time management. After all, they are legal adults, they are not first years, and they have chosen to continue their education despite the financial burden and other constraints. More than that, almost all of my graded assignments with significant weight in the class are essay based, which means I can get a feel for the students’ writing voice and it is really easy to identify plagiarism by the change in tone or maturity of the writing. If being able to turn in an assignment late meant students’ could copy each other’s assignments, I should be able to catch it even without the online plagiarism checking software.

I was concerned that I would receive all the assignments on the very last day, and was dreading the avalanche of grading that would unleash on me. Instead, assignments trickled in on a regular basis, several hours to several months late depending on the students’ circumstances, some of which were later disclosed to me. Instead of getting sloppy, thrown-together assignments, I think the quality of writing and the depth of student critical thinking were improved. Students later reported being able to spend more time on the assignment when they had control over when that time could be spent. And, despite having the most students in the most difficult semester to get through, I discovered no instances of plagiarism.

I think I will make the move to suggested deadlines semi-permanent (some deadlines will be enforced based on if it is time-sensitive). The online teaching software I use can be set to assign a 0 to missing assignments, to email me when submissions are received, and to add conditions to submission portals, such as having first submitted another assignment or having received feedback on a previous assignment (like a previous draft of a paper). I can schedule automatic email reminders about assignments, email only students who are missing assignments, and students can check their grades and assignment lists online at any time. Not only does this dramatically reduce the time I spend chasing after assignments, but it gives students more agency in being able to participate in the class on their own time.

Certainly not every class can be structured this way or allow for flexible deadlines. But, I think a lot of them could be, and I think in most cases it would improve student engagement and learning outcomes. Below, you can find the comments on my two fall course evaluations, and you can check out my previous posts on curricula development or my teaching statements.


For much of the fall semester, assignment deadlines were open ended. Do you think keeping open ended deadlines (as in, you turn in things when they are ready but [not] on a specific date) next year would make this class better? Do you think you would be able to keep up with assignments without deadlines? Or do you think the deadlines help keep you on track?

My question from the course evaluations for this fall

Comments

  • I think the soft deadlines kept me in check, however it’s nice to know that if things unexpectedly get crazy for me that I won’t be penalized for taking extra time to make sure that I submit quality work.
  • I very much appreciated the flexibility in deadlines for this class as many other classes ramp up at the end of the semester. I felt as though I could control my workload with the assignments set up like this, and would recommend keeping the deadlines as suggestions to where you should be up to date in the course, but the actual submission deadline remains later in the semester.
  • You could do once a month check ins or something to verify nobody is completely slacking off. Maybe have three major deadlines to force people to keep up – one at the end of October, end of November and then the final submission?
  • The deadlines really helped keep me on track. Dr. Sue Ishaq was more than lenient with due dates and the work load, so I do not think anyone would have an excuse to not do well in this course (although this was really helpful with the troubling times humanity is facing). I think being more strict would be more fair to her as a professor and would help students not take advantage of being able to put things off and not learn the material.
  • I think the open ended deadlines was really helpful. It allowed me to put the time in when I could rather than rushing to get it done and turned in for the due date.
  • I appreciated having the due dates so I could try to get stuff in at a reasonable time but also that the deadlines were flexible so if something came up I wouldn’t turn in something I wasn’t happy with. I had a different class with no deadlines and it was horrible, I need the structure to be there but to also have the leniency for when things aren’t going well.
  • In this new quarantined world, the open deadlines were essential to academic success. While I didn’t struggle in this class necessarily, I did struggle in chemistry, pre calculus and lab with out the aid of study groups, math labs, and lab partners. Having open dead lines in this course not only affected my academic success in this course, but it also snow balled in a positive way and helped my GPA overall.
  • I think open ended deadlines with a suggested deadline would be the most helpful, because it will reduce the stress of deadlines, and allow for leeway in the case of multiple courses having work do on the same day, but it also gives a time frame around when the work should be done
  • The lack of deadlines required self–discipline but also removed the daunting aspect of the due date, which I often find myself deterred by and ultimately more likely to put off the work. I felt that the assignments were more inviting this way.
  • I think that this semester it was very beneficial to have the open ended deadlines. For me personally, I prefer to have deadlines to keep me on track, but I appreciate the flexibility of the open–ended deadlines.
  • I think having the open ended, suggestive deadlines made for a much easier semester. It took off a lot of stress to know that I could have an extra day if needed. Sometimes we get peaks in the semester where we’re slammed with work and knowing that if I needed an extra day or two to complete an assignment was really reassuring.
  • Thank you for being understanding on deadlines as this semester has been crazy, although the soft deadlines kept me on track without penalizing me for taking extra time if needed.
  • I think ended open deadlines do help due to things become crazier as the whole covid thing continues
  • I feel that open ended deadlines next year would make this class better because due to recent events in the world it is sometimes difficult communicating with project mentors. By having open ended deadlines, I know when it is supposed to be due, but if I am missing some information from someone on the project I do not worry as much about getting in trouble for handing it in late.
  • yes this is hard to juggle long term projects with weekly class deadlines. So open ended is the best for this class.
  • I believe the structure of fall semester deadlines was great.
  • I feel like open ended deadlines are very helpful because you would be able create better quality work with your research. I feel like I would be about to keep up with work without deadlines or just create the deadline for the end of the semester and put reminders.
  • I think a more strict set of deadlines could’ve been helpful as far as tracking progress. Exceptions could still be made for those struggling on a topic, or who are unable to start for some reason out of their control.
  • This semester, while everyone has been adjusting to the new way of pandemic life, the open ended deadlines were extremely helpful and stress relieving.
  • yes I think there should be soft deadlines, there is a date that it should be done but we didn’t have to have it done by then
  • Having a general guideline about when things should be turned in has been helpful, but keeping the deadlines open ended has relieved a lot of stress and has enabled me to produce better work because I was not rushed.
  • The deadlines kept me on track and having no deadlines would have me just turn everything in at the end which is bad.
  • I liked the deadlines. I would have kept all the work till the last minute if we didn’t. However, the open ended deadlines meant that even if you were behind, you wouldn’t be penalized which really helped.
  • I think open ended deadlines are a great idea because it allowed me to not feel pressured to submit something that I did not feel was ready. Without that stress, I was able to submit all of my assignments on time with the open ended deadline and not during the later one, which was helpful!

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How to choose a graduate program in STEM

I frequently receive requests for advice on choosing graduate programs, or to work in my lab, and have conversations with graduates who are struggling with program, department, or university policies which they were not aware of when they began. I decided to put those thoughts and conversations in one place, to create a non-exhaustive list of advice and considerations for choosing a graduate program. This will mostly be applicable to STEM programs, but some aspects will be universal.

Some of this will be discouraging, because graduate school is not a thing to be entered into lightly. But, I also believe that anyone can participate in science, and that many times when people think they couldn’t succeed in science, it’s not because they aren’t good enough, it’s more of a problem with an environment that selects for just one type of researcher.

Define your goal.

What do you want to do with your career and why do you need to go to graduate school to accomplish this?

I spend more time talking people out of graduate school, or into a lesser commitment, than I spend convincing people to go to graduate school, because there is an inflated sense of the need and prestige of having a graduate degree. And, many people assume they need a degree, or the highest degree available, to get the job they want.

When I was in 6th grade, I decided I was going to be a veterinarian because I wanted to help animals, and I refused to consider other career paths which felt like a lesser calling. Three weeks into my undergraduate degree in animal science, I realized that the reality of being a veterinarian is very different from its portrayal, and it wasn’t what I wanted at all. I had only thought I wanted it because I had gotten a very limited exposure to career choices prior to going to college. I see the same mistake with people considering, or in, graduate school. I don’t mean to disparage having a veterinary or graduate degree, I just mean that the way they are portrayed to prospective students is not always accurate. Do your homework before committing to those career paths.

More than that, when you receive career advice or look into career paths, the advice tends to focus on the highlights or major types of jobs and ignore the nuance of interdisciplinary or support-level careers. Not only does this mean that everyone in animal science thinks they can only be a veterinarian or a professor to be in the field, but the way that careers are portrayed makes students think that the only suitable use of their time, and justification for massive financial burden of higher education they incur, is to go for the career with the highest prestige – whether they want that or not. Unfortunately, when students realize they don’t have the grades and the accolades to make it into the career with the most prestige, which also has the most strict entry requirements, it means students are more likely to give up entirely, consider leaving their degree unfinished, and feel guilt or shame for having failed. But here’s something no one tells you up front: choosing a different job doesn’t mean you failed to be the boss, it means you chose a different job. A veterinary technician isn’t a failed veterinarian, and a laboratory technician isn’t a failed researcher, they are performing different functions in a setting which requires collaboration from various job types.

So, I’ll ask you again, like I ask all prospective graduate students: what do you want do with your life, and do you need graduate school to get you there? This question helps you focus on creating stepwise objectives to meet your goals. Maybe you need a specific degree, or a degree in a specific field, or don’t actually need a degree at all, maybe you need an internship or professional training, and those might require a specific order to the events. Do you want to travel for work or not? Do you want to have clear definition of your job responsibilities, or the flexibility to determine your own to-do list? Do you want to be at the bench, in the field, or at the keyboard and to be doing the research, or do you want to be writing proposals and papers, and administrating the research and the lab personnel? And, do you actually want to work alone or are you alright in a social environment? Spoiler alert, most jobs in science actually require daily socialization, communication, and presentation.

All of these aspects will determine the particulars of what you need out of a graduate program and the type of degree you get. It’ll also help you in the future when you need to decide if you have met your grad school goal and are ready to move to the next phase of your life.

You can probably outline your personal goals and constraints, but defining your professional goals will take some homework. I’ve previously described the academic ladder, with descriptions of responsibilities of students, post-doctoral researchers, adjuncts and researchers, and tenure-track faculty. I have also compiled some “science journeys” into a video. Professional research blogs can be a good way to learn about life in academia, although keep in mind many labs only post about their successes and not about their failures. You can also connect with faculty on campus, and most labs will take on undergraduate (or even high school) students to participate in research. If you aren’t sure if you would be interested in research, you can ask to shadow researchers in the lab, attend a few lab meetings, or otherwise participate in a voluntary and commitment-free capacity. There are also plenty of research opportunities off campus, as well.

Volunteering for Adventurers and Conservationists for Science, collecting water samples to look for microplastics. Photo: Lee Warren.

Define your limits.

Graduate programs can be demanding, and you may need to relocate to find the topic, project, and mentor who is right for you. Before you start applying everywhere and racking up application fees, think about your constraints, your limits, and what would be a “deal-breaker” for you. Defining your limits (especially if you have a lot of them) will feel like you are writing yourself out of the possibility of finding a graduate program that works for you. In reality, it will help you find an institution that matches your life better and will help you focus on what is really important to you. You don’t have to erase all other aspects of your life in order to be a scientist.

Often, you feel pressured to give up everything to go to graduate school or other professional degree programs. The perception is that because there are fewer available positions than applicants that you need to underbid everyone else and give up everything, essentially that you need to recruit the graduate program. You assume you have to relocate and out of your own pocket, you need to put family on hold, you need give up job benefits, and you will have to work all the time.

I’ve moved over 7,000 miles for academic jobs.

Some of that may be true, and you should think about what you are able to manage and what you can’t live without. Some of that is just perception cast by work-a-holic culture and you will be able to reject or negotiate aspects. Think of your list of limits as conditions your employer might need to meet in order to convince you to take the position.

Narrow down your interests.

What do you want to do day after day, failure after failure?

If you start to make a list of things you are interested in science and you start writing down all the cool things you saw on social media – stop right there. Science is cool, but most of the time is cool in retrospect after the work has been completed and narrative added in. Science is arduous, iterative, and requires a lot of process improvement and reflection, and that takes time and focus. You need to be able to work on the same thing day after day and maintain interest even if everything you do seems to fail everyday. Especially when you are trying to develop technical skills and analytical skills, you need to be able to focus and dive deep into your topic, and you can’t be distracted by every little thing you think is cool, otherwise you will never get anything done.

You don’t need to commit to your research interest for life, and you don’t need to have an incredibly narrow scope to your interests, but you should be able to identify a common theme or the aspect that draws you in. Which topic makes you ask “yes, and?” over and over. What cool science story made you look for a second similar story, and then a third?

Search for a program.

There are a few different types of graduate degrees available, and each have nuances about the requirements to get in, requirements to graduate, cost to you, salary and benefits to you, and approach for application and acceptance into the program. I recommend looking into programs first, to find a location and institution that best meets your personal and professional goals and limits, and then trying to find a mentor. Don’t underestimate the importance of geographic location, and the environmental and social climate you will find there. You might need to be close to family, or find a location with a job or program for a partner. And if you are used to sun, several years of overcast winters might lose their novelty.

Most people apply to multiple programs and it can take time to find the right match. If you end up applying to multiple programs at a single institution, you can ask them to waive additional application fees, something that is commonly done but not commonly advertised.

Masters of Professional Studies are designed to give you familiarity with research and build skills. MPS is not thesis-based and requires research participation but not your own research project, so it is often used for people who will be in research-adjacent jobs. Students are admitted to programs based on their GPA, exam, or other numeric qualifications, and during their first semester have to identify a research mentor and two other committee members to guide their curricula and career development. MPS students pay for their own tuition, and most program/university policies stipulate that they are not allowed salary for their research, although they usually can be paid summer research salary. MPS students are eligible for teaching assistantships, but few, if any research assistantships. Because you are categorized as students and not employees, you do not receive health insurance or other fringe benefits, but you are eligible for student health insurance plans. MPS are completed in 2 years, but can be completed over longer periods of time to accommodate working professionals.

Master of Science programs are thesis-based, and require research study in a project you co-lead. Applications may be accepted year-round or according to deadlines, depending on the program. Master’s programs are designed to last 2 -3 years (credit hour requirements make it almost impossible to accomplish in fewer than two years), and beware mentors or projects which assign you a PhD-level amount of work to accomplish in just two years. Finding funding for master’s programs can be tricky, as many universities prioritize PhD students in order to boost their Carnegie research rating, but master’s programs are needed for training the majoring of the research workforce. Typically, you are paid a salary for your master’s, including partial coverage of your health insurance, and full coverage of your tuition. Most programs do not cover full health insurance, or semester fees, both of which can cost a thousand dollars of more in each of the spring and fall semesters, but you might be able to negotiate these to be paid by your advisor. You are considered both a student and an employee, but most university policies make graduate students ineligible for university-based or even individual-based pre-tax retirement savings programs for employees, although you can configure a post-tax retirement savings plan on your own.

Doctorate of Science programs are dissertation-based and requires that you (more or less) lead a research study and have contributed significantly to the theory behind its design, or theory behind its analysis and interpretation. PhD programs are designed to take about 5 years in the US (3 years in many other countries which don’t require coursework). Credit hour requirements make it almost impossible to accomplish in fewer than 4 years in the US, and PhD time can vary between 4 – 9 years, depending on the research and other circumstances. Applications are accepted year-round for direct-to-lab admissions (see below), and once or twice a year to be considered for lab-rotation-based fellowships.

Thesis-based science programs have two paths to admission, which is not always common knowledge. You will always have to apply to the graduate college of a university and meet the qualifications set by the university, as well as the program/department. After passing initial qualification checks, the graduate school will forward applications to the department to review, and it is this step that offers two paths.

If graduate programs have a collective fund to support students (teaching or research assistantships), they might accept a certain number of students as a cohort based on their qualifications. The top number of applicants will have some sort of recruitment event in which you are shown the facilities, have a chance to talk to students and faculty, and are interviewed by the program admission committee. Applicants who are admitted as a cohort have salary provided for the first 1 – 2 years as they take classes and rotate through different research labs. At the end of rotations, you match with a lab that has money to continue funding your salary and your research. Most programs will not accept so many students to the cohort that they will be unable to find them funding to continue their graduate work.

However, because thesis-based study is a funded position, you might apply to a department as a “direct admission”. This means that you have already matched with an advisor during prior conversations, the advisor has already looked through your application, and that the advisor and the department have informally agreed to offer you a position. But, this method is entirely dependent on that advisor having funding to pay your salary, tuition, and your research costs. You need to start the conversation with a possible mentor 6 months or more before you want to begin, unless you are applying to an advertised position in their lab. Finding research funding takes 6 – 18 months because of the slow pace of federal funding review and allocation, so if your advisor needs to find funding it will take planing ahead of time. Direct admission can happen on a rolling basis, but you will still need to apply to, and meet the qualifications of, the graduate college. Because of the unpredictable nature of the funding, you can defer a direct admission offer for a year, as needed.

Interviewing and searching for a mentor.

Whether you are applying as part of a cohort or a direct admission, you will have some sort of interview. It might be a series of informal conversations with potential advisors, or a formal interview with a program admission committee. When you are going into a graduate program interview, it feels daunting, and it’s not until you advance your career enough to be on the interviewer side that you realize it is supposed to be a conversation and not a test.

The graduate interview is not really about proving your qualifications because you have already met that hurdle with your application. The interview is to match students to mentors, and to confirm your interest in research. By having conversations and interacting in real time (whether in person or via electronic chat), interviewers can assess your communication skills, and get a better idea of your goals and interests.

The graduate advising relationship is quite different from what you might have experienced with previous instructors or undergraduate advisors, so it’s important that your personal and professional goals line up with those of your advisor. It really helps if you actually get along. You’ll be working together for several years during your degree, and will maintain a mentoring relationship for a good portion of your early career after you graduate. As a member of their lab, you’ll be performing a lot of their research and representing them at conferences and other venues during presentations, collaborations, or future work. It’s important to your career and theirs that you are able to work well together.

Therefore, during your grad school interviews you should remember that you are interviewing them, as well. The interview is an opportunity for your future advisor and institution to impress you and convince you to take a position with them. This is your chance to ask them about the projects you might be doing, where former lab members are now, their expectations of you, and more. Many federal funding proposals require a detailed mentoring plan, so advisors already have an idea what your professional development might look like. Importantly, get an idea about the lab culture. Some advisors feel you should work nights and weekends and during all breaks, others feel that your contributions belong to the lab and you might not have as much access to your own intellectual property than you think. And, not every lab has made a commitment to equity and inclusion. Here’s the policy for the Ishaq Lab.

It’s also a great time to ask grad program coordinators about university policy, departmental expectations, and financial support opportunities which might affect you. Does the program provide some or all financial support for health insurance, tuition, salary, and student fees? If not, what opportunities are in place to secure these? Are you able to switch mentors if there is a professional or personal mismatch? Is childcare available for graduate students? What about time off for maternity leave, and is this paid or unpaid? Family or medical leave? What if you need to take a semester or a year off, can you get back into the program and would you lose your funding? How many papers will you need to publish, or scientific presentations to give, and will there be financial support for those costly endeavors? While no one would ask you to pay publication fees out of pocket, I have heard of researchers refusing to financially support grad student travel to conferences, despite many departments requiring students to present in order to obtain their graduate degree. Travel to scientific conferences can run to several thousand in travel and participation costs per trip, and one trip to a national-level conference could cost an entire month’s graduate student salary.

Adopt healthy habits.

If everything comes together and you’ve been accepted into a graduate program that works for you, congratulations!! I wish you the best on the next step of your journey. If you are looking for more advice for once you get there, check out my previous posts, including preparing yourself before you start by adopting good habits for organization and work-life balance.

Reblog: “Animal and veterinary sciences seniors: Capstone stories”

Starting this fall, I have been teaching the UMaine Capstone Experience courses for Animal and Veterinary Sciences students (AVS 401 and 402). To complete the University of Maine requirements for graduation, students must participate in a Capstone Experience to knit together the work of their undergraduate degree into a cohesive project. AVS students are required to part pate in research under researcher mentorship. Some of those students felt comfortable sharing short descriptions of their project. The slightly edited summaries and my intro were posted to the University of Maine news page for teaching experience updates.

Teaching Statement development series: evaluating my approach

This is the final installment of the selected portions of my Teaching Statement as part of a development series, drafted 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.*


Evaluating my approach to teaching (modified to remove sensitive information)

I regularly solicit student feedback in my courses, either in class, or via anonymous surveys using online teaching platforms (Brightspace), to improve the quality and content of my teaching materials.  For example, a voluntary, anonymous survey of AVS 401 Senior Paper in Animal Science I students in fall 2020 on lecture content and order revealed that the material presented (see Developing curricula) was all or partly new to them, that they would have preferred to learn about Project Management and Experimental Design earlier in the lecture series, and that they found all lectures to contain useful information. Survey report available upon request. Student comments included

  •  [ Student comments redacted for the blog post]

Similarly, I solicit feedback from my peers, including an ad hoc Pedagogy in STEMM working group on campus.  The working group meets semi-weekly to discuss curriculum development, and in particular, including social issues into science courses. I led a one-hour meeting on re-thinking tense classroom conversations, as well as making student contribution equitable and productive. My re-devised strategy, a 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. 

Finally, the use of online teaching software (Brightspace) allows me to evaluate student engagement in real-time, from tracking assignment submission times, to identifying patterns in grading that point to poorly-worded or confusing assignments, to participation in online discussion forums by topic.  The software facilitates tracking progress by individual students or the class over time, allowing me to parse when I need to reach out to offer additional help, or when I need to change an assignment deadline because it conflicts with large assignments (such as mid-term exams) from other courses which divert student attention. 


Previous installments:

Teaching Statement development series: science and society.

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: 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.

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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