Looking back on my first year as an assistant professor

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

View from the bridge in Orono.

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

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

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

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

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

Bring a campus map

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

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

Do not neglect the mountain of paperwork

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

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

Take time to generate new materials

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

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

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

Ask for help

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

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

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

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

Level up your time management

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

Image source, Pixabay.

Leave yourself plenty of flexibility in your schedule

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

Track everything you do

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

Be kind to yourself

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

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

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

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

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

View of a wooden deck with forest behind it.

What is academic Outreach/Extension?

Service can be a vaguely defined expectation in academia, but it’s an expectation to give back to our community; this can be accomplished in different ways and is valued differently by institutions and departments.  Outreach is an easily neglected part of science, because so often it is considered non-essential to your research.  It can be difficult to measure the effectiveness or direct benefit of outreach as a deliverable, and when you are trying to hoard merit badges to make tenure and your time is dominated by other responsibilities, you often need to prioritize research, teaching, advising, or grant writing over extension and service activities.  Nevertheless, public outreach is a vital part to fulfilling our roles as researchers.  Academic work is supported by public funding in one way or another, and much of our research is determined by the needs of stakeholders, who in this sense are anyone who has a direct interest in the problem you are trying to solve.

Depending on your research field, you may work very closely with stakeholders (especially with applied research), or not at all (with theoretical or basic research).  If you are anywhere in agriculture, having a relationship with your community is vital.  More importantly, working closely with the public can bring your results directly to the people out in the real world who will benefit from it.

A common way to fulfill your outreach requirement is to give public presentations.  These can be general presentations that educate on a broad subject, or can be specifically to present your work.  Many departments have extension specialists, who might do some research or teaching but whose primary function is to connect researchers at the institution with members of the public.  In addition to presentations, extension agents generate newsletters or other short publications which summarize one or more studies on a specific subject.  They are also a great resource for networking if you are looking for resources or collaborations, for example if you are specifically looking for farms in Montana that grow wheat organically and are infested with field bindweed.

For my new job, I’m shifting gears from agricultural extension to building science and health extension.  In fact, the ESBL and BioBE teams at the University of Oregon have recently created a Health + Energy Research Consortium to bring university researchers and industry professionals together to foster collaborations and better disseminate information.  The goals of the group at large are to improve building sustainability for energy and materials, building design to serve human use better, and building microbiology and its impact on human health. I have a few public presentations coming up on my work, including one on campus at UO on Halloween, and one in February for the Oregon Museum of Science and Industry Science Pub series in February.  Be sure to check my events section in the side bar for details.

Even when outreach or extension is not specified in your job title, most academics have some level of engagement with the public.  Many use social media outlets to openly share their current work, what their day-to-day is like, and how often silly things go wrong in science.  Not only does this make us more approachable, but it’s humanizing.  As hard as scientists work to reach out to the public, we need you to reach back.  So go ahead, email us (please don’t call because the stereotype is true: we really do hate talking on the phone), tweet, post, ping, comment, and engage with us!!

 

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Presentation on maternal influences on the calf digestive tract from JAM 2016 available!

The video presentation of my work on the effects of maternal biotic influences on the developing calf digestive tract bacteria is finally available for public use!

Abstract 1522: Influence of colostrum on the microbiological diversity of the developing bovine intestinal tract

Suzanne L Ishaq, Elena Bichi, Sarah K Olivo, James Lowe, Carl J Yeoman, Brian M Alridge

 

The Interviewing Game

Interviewing for research positions is challenging, and when it’s for a job at a university, the process can be lengthy and the competition fierce.  Some jobs for which I applied reported receiving 60 to 160 applications for a single opening.  When it comes to highly coveted positions, like tenure-track faculty jobs, the slow reduction in research funding and ever-increasing pool of PhDs can result in up to 400 applications per opening.  One faculty member eloquently provided stats on their job search, which involved more than 100 applications over two years.  I applied to a mere 22 jobs over a period of seven months (just counting the 2016-2017 season), but the lengthy process generated plenty of questions from family and friends who were dismayed by the slow trickle of news.

The Search Committee

The job posting needs to be carefully crafted.  While most academic positions are looking for candidates with specific skills or research backgrounds, many faculty positions are open-ended so that a wide variety of candidates may apply.  Any required elements of the job, such as teaching specific courses, advising, or extension activities, are often explicitly stated in the posting.  Once funding for a job position and a post has been approved, the search officially opens.  A search committee is formed, which is comprised of several members of the department, and perhaps members of other, closely related departments at the university.  They may aid in the drafting of a job posting, but will be in charge of reviewing every application, selecting candidates for and performing preliminary and full interviews, following up on references, and making final recommendations.

The Application

Applications require a Curriculum Vitae, which lists your education and other professional training, all the positions you have held, professional memberships you belong to, certifications, awards, publications, public presentations, courses taught, career development activities, students you have mentored, and any other skills that might be relevant.  Some applications require official transcripts, and all require letters of reference.  These may need to be provided at the time of the application, or may be requested later by the committee when you have been added to the short-list of potential candidates.  Your letters of reference not only confirm the skills you have claimed in your application, but they provide a glimpse into what it is like to work with you, so it’s best to pick someone who knows you well.

The brunt of the academic application is several essays that detail your experience, philosophy, and vision for each aspect of the job in question.  Some universities limit these to one to three pages each, but others allow you the freedom of word count.  Typically, you must provide a Statement of Research and a Statement of Teaching, and some may request Statements of Mentoring, or Diversity.

The Statement of Research asks you to detail previous work, the skills you have acquired, and important contributions your research has made.  Here, you outline your experience in obtaining grants, or your plan to obtain them in the future, as well as describe the work you would like to perform at the university and the lab members you would like to bring in (undergraduates, graduates, technicians, postdocs).  Outlining your proposed research can be tricky,  as you want to add your expertise to the ongoing departmental research, but without being redundant or too novel.  That might seem counter-intuitive, but if a department doesn’t have the equipment or funding to support your research, or similar researchers that can provide a research support network, it may be difficult for you to perform your work there.

Similarly, the Statement of Teaching asks you to explain in detail your previous teaching experience, and your philosophy of how courses should be developed to improve student learning, incorporate current research or hands-on experience into the curriculum, and use technology to increase student engagement.  Here you can suggest courses that you would like to develop or take over teaching, based on your knowledge base, if the position involves teaching.

Additional Statements may be requested to provide specific information on your philosophy of mentoring students, especially your Statement of Diversity for training new graduate students, or recruiting minority students to science and providing career development opportunities to underrepresented demographics.  The cherry on top is the cover letter that summarizes why you want the job and why you are the best choice.

The Wait

Applications may be solicited for several weeks or months, and some accept applications on a rolling basis until the position is filled.  You will receive a notification, usually automatic, that your application has been received by the system, and perhaps another one to notify you that the review has begun.  Otherwise, you have little communication unless you are selected for the short-list or the position has been filled.  I have waited more than 6 months to hear back about an application before.

It’s time to meet our first three eligible candidates…

The short-list is a subset of applicants, several or several dozen perhaps, that the committee would like to have a phone or video interview with, typically lasting 15 to 60 minutes.  Depending on the number of applications received and when the job posting  closed in relation to the end of the semester, you may not hear about a preliminary interview until several months after you have applied.  Questions requiring detailed answers are often provided in advance, but otherwise, preliminary interview questions usually ask you to reiterate what you might have put in your application: why you want the job, whether you have experience working collaboratively, where you see yourself in five years, etc.  These questions may probe your interpersonal skills, such as whether have you managed others, or whether you have dealt with academic conflicts.  Having been through a number of tele-interviews, I can say that they are more difficult than they seem.  You have a brief time in which to make an impression, and it can be difficult to read a room which you can’t see.

Round 2

From the short-list, two to four candidates are selected for full, in-person interviews, which are scheduled as soon after the phone interviews as possible.  These are complicated to schedule, as they are one to two full days for which the candidate and most members of the department need to be available.  You are required to present a seminar of your research, both past and future.  Depending on the position, you may be required to present a teaching seminar as an example of your style, or perhaps a “chalk-talk” where the committee can ask you questions on potential grants or experimental designs.  You will also have one-on-one interviews with university faculty and staff that you may be working with, tours of the research facilities, and a chance to tour the university.  From experience, even when the interview goes perfectly, they are exhausting. For two days straight you are talking about yourself, your work, your ideas, other people’s work, and potential collaborations.  You are listening attentively, trying to give the best impression possible, and eating meals as quickly as possible while still talking about yourself and hoping you don’t have food stuck in your teeth.

Only once all the selected candidates have been interviewed will the search committee deliberate.  They solicit impressions and opinions from everyone you met- faculty, staff, graduate students, technicians, as well as from your professional references.  They will decide if a candidate is ineligible for an offer for any reason, and rank the eligible candidates.  They will then make recommendations to the department chair or administrator, who will decide whether to extend an offer.

Negotiations

When a job offer is first made, it is a non-binding offer.  Negotiations then take place until both parties are satisfied, and a written, contractual offer will be offered.  University positions have salary ranges by hiring level and experience, and a certain, somewhat unknown, amount of additional funding available for other benefits like relocation, computers, or basic research materials.  Tenure-track or other high-level research positions in the STEM fields typically come with start-up funds, which provide initial funding to buy equipment and lab materials, or fund lab personnel to get you started on pilot studies that can be leveraged for grant funding.

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http://www.glasbergen.com

This is the most delicate phase because this is your best chance to determine your salary, your title, and the specifics of your job requirements.  For example, you can use this opportunity to discuss when and how much you will be asked to teach, what your start date is, whether the department will reserve a teaching or research assistantship so that you may offer it to a new graduate student, and other non-specific benefits.  If you have multiple offers, you might ask one to meet the benefits proffered by another.  On the other hand, universities only have so much they can offer you, regardless of how much they like you.  Remember, you aren’t out to “win”, you are out to satisfactorily arrange a contract with the people you will soon be working with- both parties need to be pleased with the offer.  If an agreement can’t be reached, or if you accept a different offer, the second-ranked candidate will be offered the job, and so on.

Nothing is finalized until both parties have agreed to terms, a background check has been completed, and the contract is signed.  From application to contract, the process may take 6 to 12 months, and it may be a further several months before you officially begin, which is a long time to provide vague answers to eager questions from friends and family.  On top of that, most interviews are semi-confidential: you are not supposed to know who the other candidates are, so it is bad form to ask about them or for the department to discuss them with you, even after you have accepted the job.  And, most applicants keep their interviews quiet until they have a job offer.  For one thing, it’s not worth getting everyone’s hopes up for every application.  For another, you don’t want a prospective job to pass you over because it looks like you are going to accept another offer, as candidate searches are expensive to conduct and occasionally don’t lead to a hire (failed search).  There is also the potential for an uncomfortable situation to arise at your current job when they know you are leaving, although the pervasive search for job security and work-life balance in academia means most people sympathize with your search for the right job.

I choose… Candidate #3!

In the end, much of it comes down to luck: the right department needs to be looking for a candidate like you and have their hiring line approved, you need to find their posting, you need to craft an application that appeals to them while representing your interests and goals, and you have little to no idea who else might be applying.  Often jobs will be posted at an open hiring level to attract a wider variety of candidates, so you might be applying at the lower hiring end but are competing with people who have years more experience than you do.  And it’s important to remember that everyone in science has a large amount of technical training – we are all fantastic candidates and that makes it difficult to choose only one of us.

Since departments or fields don’t relist open positions predictably, most research job hunters will apply to jobs in their field to cover your bases, as well as several closely related fields (for me, it was animal science, microbiology, molecular genetics, microbiomes, bioinformatics, and any combination of those words); you are afraid to lose a whole year because you didn’t apply to enough postings.  This increases the applicant pool size, and provides departments with interesting research directions to take the potential hire in; sometimes you don’t know what kind of candidate you want until you meet them.  Moreover, you don’t really know if you will fit with a university, department, or research team until you have had some time to interact with them during the interview.  Really, applying for a job in academia is a lot like dating.  Some people go on many first date interviews, some on very few, in order to find the right match.  Either way, it’s fun to play the game, but to win you need to ‘make a start date’.

Featured Image modified from The Dating Game show logo.

I’m now writing for the UO BioBE blog

The Biology and the Built Environment center here at the University of Oregon has a blog, and I’ll be writing updates and blog posts for them, as well.  I will be cross-posting my posts, but you should also check them out!

My review on Plant-Microbial Interactions in Agriculture got published!

A few months ago, I was invited to submit an article to the special issue “Plant Probiotic Bacteria: solutions to feed the World” in AIMS Microbiology on the interactions between agricultural plants and microorganisms.  As my relevant projects are still being processed, I chose to write a review of the current literature regarding these interactions, and how they may be altered by different farming practices.  The review is available as open-access here!

“Plant-microbial interactions in agriculture and the use of farming systems to improve diversity and productivity”

A thorough understanding of the services provided by microorganisms to the agricultural ecosystem is integral to understanding how management systems can improve or deteriorate soil health and production over the long term. Yet it is hampered by the difficulty in measuring the intersection of plant, microbe, and environment, in no small part because of the situational specificity to some plant-microbial interactions, related to soil moisture, nutrient content, climate, and local diversity. Despite this, perspective on soil microbiota in agricultural settings can inform management practices to improve the sustainability of agricultural production.

Keywords bacteria; climate change; farming system; fungi; nutrient exchange; pathogens; phytohormones

Citation: Suzanne L. Ishaq. Plant-microbial interactions in agriculture and the use of farming systems to improve diversity and productivity. AIMS Microbiology, 2017, 3(2): 335-353. doi: 10.3934/microbiol.2017.2.335

Expanding Your Horizons for Girls workshop, MSU 2017

Yesterday I participated in the Expanding Your Horizons for Girls workshop at Montana State University!  EYH brings almost 300 middle-school aged girls from all over Montana for a one-day conference in STEM fields.  Twenty-seven instructors, including myself and other female scientists and educators, ran workshops related to our current research.  My presentations were on “Unlocking the Hidden World of Soil Bacteria”, with the help of undergraduate Genna Shaia from the Menalled Lab.

I gave the girls a brief presentation on microbial ecology, and how bacteria and fungi can affect plants in agricultural soil.  We talked about beneficial versus pathogenic microorganisms, and how different farming strategies can influence soil microbiota.  This was followed by two hands-on activities that they were able to talk home with them.  First, the girls made culture plates from living or sterile soil that was growing wheat or peas to see what kind of microbes they could grow.  Then, they planted wheat seeds in either living or sterile soil so they could track which soil made the seeds germinate faster.

 

The girls were enthusiastic to learn, asked lots of insightful questions, and it was awesome being able to share microbiology with kids who hadn’t given it much thought before!  If you are a woman in STEM, and have the opportunity to participate in a workshop or mentor a young scientist,  it is not only rewarding but can make a huge impact on encouraging women into STEM.

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Slideshow photos: Genna Shaia, reproduced with student permission.

2017 Congress on Gastrointestinal Function

I just got back from my very first Congress on Gastrointestinal Function, poster tube.jpga small meeting for  researchers with a specific focus on the gastrointestinal tract, which is held every two years in Chicago, Illinois.  The special session this year was on “Early Acquisition and Development of the Gut Microbiota: A Comparative Analysis”.  The rest of the sessions opened up the broader topics of gut ecosystem surveillance and modulation, as well as new techniques and products with which to study the effect of microorganisms on hosts and vice versa.  The research had a strong livestock animal focus, as well as a human health focus, but we also heard about a few studies using wild animals.

As I’ve previously discussed, conferences are a great way to interact with other scientists.  Not only can you learn from similar work, but you can often gain insights into new ways to solve research problems inherent to your system by looking at what people in different fields are trying, something that you might otherwise miss just by combing relevant literature online.  A meeting or workshop is also a great place to meet other similarly focused scientists to set up collaborators that span academia, government, non-profit, and industry sectors.

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It was great to catch up with Dr. Ben Wenner, now at Purdue Agribusiness, and meet Yairy Roman-Garcia, grad student at the Ohio State University.

This year, I was excited for one of my abstracts to be accepted as a poster presentation, and honored to have the other upgraded from poster to talk!  Stay tuned for details about both of those projects in the coming weeks, and be sure to check this meeting out in April, 2019.

If at first you don’t succeed… you’ve got the makings of a thesis.

In a recent post on The Rare Knowledgesphere, I mentioned that I when I tell people that I went to graduate school or explain what I do now, the replies can be overly modest or self-deprecating.  Sometimes, people tell me that they don’t feel smart enough to make it through grad school or to do what I do.  Graduate school or other professional schools aren’t for everyone, but there is a big difference between not wanting to go and not feeling good enough to go.  In my experience, people who think they can’t do it aren’t so much incapable as incapacitated by Imposter Syndrome.  In my 9 total years of acquiring higher education, plus 2 years and counting of post-doctoral training, I find that when it comes to academic success, academic achievement frequently takes a backseat to having the right personality.  In this post, I thought it would be helpful to describe some of those qualities that help set the most successful researchers apart.

Learning is a skill

Don’t get me wrong, you need to pass the graduate record examinations (GREs- general and subject) in order to be accepted, be able to understand the material once you are there, do well on exams, and maintain a certain grade point average (GPA).  While grades and exam performance can be good metrics for intelligence, there are a lot of circumstances that could preclude someone from doing well, thus they aren’t the only metrics.  Certainly you need a solid knowledge base in any subject in order to participate in it.  But I don’t usually get asked by people I pass on the sidewalk to explain how 20 different enzymes react instantaneously when you consume a meal in order to alter your metabolism to maintain homeostasis.  I am asked on a daily basis to assimilate new information, process it, and then apply it to my work.  Whether it is learning a new skill (like learning to perform a laboratory technique or how to analyze data I have not worked with before), whether it is evaluating a proposed experiment and looking for flaws in the experimental design, or whether it is reviewing someone’s manuscript for validity and publish-ability, I need to be able to learn new things efficiently.

Learning is a skill, just like wood-working or weight-lifting: you need to start small and practice regularly.  Learning a new skill, language, or activity challenges us.  Not only can it broaden our view of the world, but continuing to learn throughout your adult life can improve health and cognitive function: essentially, the more you learn the better you become at learning.  In addition to physically performing new tasks, reading is a great way to inform yourself while improving your reading comprehension skills, verbal IQ, and  critical thinking so that you can assess the accuracy of the information.  Scientific texts, even for those who are trained to read them, can be extremely difficult to fully comprehend.  Articles are full of very technical language, explain new concepts, and often rely on a certain amount of knowledge inherent to the field.  It’s tempting to read quickly, but in order to do this you efficiently it can help to be systematic and thorough.

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You may not feel you are ready for graduate school, that you belong in grad school, or that you are ready to leave, but grad school isn’t the end point- it’s a learning experience to become a good researcher.  Even once you leave, you never stop learning.  Good graduate students don’t have to know everything, but they do need to know how to learn and how to search for answers.

Put on a happy face

You don’t need to love grad school, your work, or the process of research every second of every day, and you don’t need to pretend to, either.  It can be difficult, and like with any job, there are good days and bad days.  A hardy personality falls a close second to being able to learn new skills.  The road through graduate school is arduous and different for everyone, and it takes a tough person to make it out of the labyrinth of Academia.  Moreover, you are truly surrounded by your peers; everyone in graduate school has already maintained a high GPA, passed the GREs, gotten into grad school, etc.  You are probably never going to be the smartest or most accomplished person in the room again, certainly not for a long time.

You need to be able to take criticism, and not just the constructive kind: not everyone maintains polite professionalization and at some point, someone will bluntly tell you that you don’t belong in graduate school.  For me, this occurred about two years in, when I submitted my first manuscript.  A reviewer mistook my statement that a certain type of photosynthetic, water-based bacteria were present in the rumen of moose (who acquire them by drinking swamp water) for saying that those bacteria normally lived in the rumen of the moose, and commented that the latter was incorrect, that I did not know what I was doing, and that I did not belong in science.  To be sure, being able to deliver information in journal articles in an accurate manner is critical, and if a reviewer mistakes what you say in a manuscript, then you need to clarify your statements.  If a journal article is found to be unsuitable for publication, the reviewer can recommend it be rejected and offer commentary on how to improve re-submissions. However, it is widely accepted to be inappropriate and unprofessional to make personal comments in a review.  I was taken aback at how one misinterpreted sentence in a 5,000 word article could lead someone who had never met me to determine that I wasn’t suited for science.

In the end, I clarified that sentence, resubmitted, and the paper got accepted.  Four years later, that article has been viewed over 6,500 times and several other papers have come out identifying bacteria of that type living in the gastrointestinal tract of animals.  Research is a competitive field, and by its nature requires repetition and trouble-shooting.  You need to be able to fail on a daily basis and still find the enthusiasm to learn from the results and try it again tomorrow.

Two heads are better than one

Working well with others is extremely important in graduate school (and really any work environment).  In graduate school, other people can challenge you, help you reason through problems, identify holes in your logic, or add a perspective based on their personal experiences.  In science, you can never be an expert in everything, and to be able to really answer a research question you need to be able to look at it from different angles, methods, or fields.  Collaborations with other scientists allow you to bring a breadth of expertise and techniques to bear in projects, and can improve the quality of your research (1, 2, 3).

However, it can be difficult to wrangle so many researchers, especially when everyone is so busy and projects may span years.  Emotional intelligence, the ability to empathize, has been found to contribute to academic intelligence and can foster interpersonal relationships and collaborations.  When money, prestige, and ideas are on the line, the drive to be recognized for your work needs to be balanced with empathy in service to completing the experiments and disseminating the results.  At some point in academia, personal conflict will jeopardize a project.  As much as you have a right to recognition and reward for your hard work, you need to remember that other project members are due the same.  That being said, as a graduate student you don’t always feel in a position to negotiate and may feel pressured to minimize your contribution or the thanks to which you are due.  Settling on an order for authorship, or credit for contributions, is a conversation that needs to happen early, often throughout the project, and inclusively to acknowledge that you all worked hard for this.

Organization

Being able to juggle taking classes, teaching and grading, performing research, attending meetings, and all the other hundred things one must do in an academic day, takes a high degree of coordination.  Your calendar is your friend: schedule everything from meetings to reminders about tasks.  And using shared calendars really helps to schedule meetings or remind others.  There are plenty of apps that are specific to laboratory scheduling needs to help coordinate meetings or assign tasks across multiple parties.

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30 Rock

Even more important these days is digital organization: whether it be your email or your hard drive.  You need to be able to confidently curate and store data or electronic materials so that you or someone else can find them, even years later.  You never know when you will need to resurrect an old project or check on a method you once used, and without a solid paper trail you may not be able to locate or understand your digital breadcrumbs.  Lab notebooks, protocols, data files, and knowledge need to be accessible to future members, and it is your responsibility to make them available and intelligible.  There is nothing more frustrating than finding an unlabelled box of samples in a freezer and being unable to identify their owner or contents.  While the Intellectual Property might be yours, if that research or your salary was paid by a university or governmental agency, you have a responsibility to make that information public at some point.

A high degree of organization can help you manage your time, keep track of your results, coordinate with others, and maintain a project schedule.

A spoonful of extra-curricular helps the biochemistry go down

Work-week expectations, course load, teaching load, research load, and financial compensation of graduate students vary by the nature of their appointment, by university policy, or even by department within a university.

Graduate Teaching Assistants are paid a stipend for providing undergraduate teaching and other miscellaneous help to the department (typically 20 hours per week), and may receive tuition compensation for the classes they take.  Depending on the nature of the program, they may do research as well in order to write a thesis (masters) or dissertation (doctorate), or not do any research for their degree (non-thesis major). Graduate Research Assistants (GRAs) are hired strictly to perform research (again, usually 20 hours per week), for which they receive a stipend and/or tuition compensation, and also take classes.  Most programs require GRAs to teach for one semester to gain the experience, and GRAs are almost exclusively performing research for a thesis/dissertation-based degree.  Regardless of the type of appointment, there are a certain number of classes and hours of research which must be logged before a degree may be obtained.  Between courses, teaching, and research, there is enormous pressure on graduate students to work more than 40 hours per week.

It might seem that immersing yourself in graduate school is the best way to be a good student.  Or, maybe you are overwhelmed by the amount of work you are being asked to accomplish and feel pressured to spend 12 – 18 hours a day at it just to meet deadlines. Firstly, you are not lab equipment and should not be treated as such.  As a student, as an employee, and as a person, you have rights in the workplace.  It’s worth looking into university policy to see exactly what it required of you.  Secondly, over-working yourself is a terrible way to be more productive, as I discussed in a previous post on work-life balance.  To summarize that post, over-working yourself negatively affects your health, your cognitive function, and the quality of your work.  On the other hand, taking regular breaks and vacation can help keep you focused and solve abstract problems.

In addition to helping you manage stress, having an active life outside of your program helps give you other experiences from which you can draw upon to aid your graduate work. For example, I worked for several years at a small-animal veterinary hospital before going to graduate school, at which I trained employees and had extensive interactions with customers.  There, I gained the skills to manage others, simplify technical information, be very specific in my instructions, or maintain a professional demeanor in the face of emotional or chaotic events.  My interests in painting and photography have improved the quality and presentation of graphical results, or visually document my experiments.

Learn to Type

Seriously.  I spend most of my time at a computer: reading, writing, cut/pasting.  If you can type as quickly as you can gather your thoughts,you’ll find that you are much more productive.

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Draft twice, submit once: the grant writing process

Today, the research team that I am a part of submitted a grant which I co-wrote with Dr. Tim Seipel, along with Dr. Fabian Menalled, Dr. Pat Carr, and Dr. Zach Miller. We submitted to the Organic Transitions Program (ORG) through the US Department of Agriculture’s (USDA) National Institute of Food and Agriculture (NIFA).  The culmination of months of work, and some 12+ hour days this past week to meet today’s deadline, this grant will hopefully fund some very exciting work in agriculture!

Research relies on grant money to fund projects, regardless of the type of institution performing the research, though commercial research centers may partially self-fund projects.  Most new research hires to universities will receive a “start-up package” which includes some funding for a few years to buy equipment, pay for a small, preliminary project, or temporarily hire a technician. Start-up funds are designed to hold a researcher over for a year or two until they may apply for and receive grant funding of their own.  Sooner or later, everyone in academia writes a grant.

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Grants may be available for application on a regular basis throughout the year, but some grant calls are specific to a topic and are made annually.  These have one submission date during the year, and a large number of federal grants are due during in the first quarter of the year, a.k.a. Grant Season.  University researchers find themselves incredibly pressed for time from January to March and will hole up in their office for days at a time to write complex grants.  Despite the intention of starting your writing early, and taking the time to thoroughly discuss your project design with all your co-PDs well before you start writing to avoid having to rewrite it all again, most researchers can attest that these 20-30 pages grants can get written over from scratch 2 or 3 times, even before going through a dozen rounds of group editing.

The Bright Idea

Most large grants, providing several hundred thousand to over a million in funding over several years, require project teams with multiple primary researchers (called Principal Investigators or Project Directors) to oversee various aspects of research, in addition to other personnel (students, technicians, subcontractors).  One researcher may conceptualize the project and approach other researchers (usually people they have worked with in the past, or new hires) to join the project.  Project ideas may get mulled over for several years before they mature into full grant submissions, or go through multiple versions and submissions before they are perfected.

The grant I just co-wrote investigates the use of cover crops in Montana grain production.  Briefly, cover crops are plant species which improve the soil quality but which you aren’t necessarily intending to eat or sell.  They are grown in fields before or after the cash crop (ex. wheat) has been grown and harvested.  Legumes like peas, beans, or alfalfa, are a popular choice because they fix nitrogen from its gaseous form in the atmosphere into a solid form in soil which other plants (like wheat) can use.  Other popular cover crop plants are great at bio-remediation of contaminated soils, like those in the mustard family (1, 2, 3). Planting cover crops in an otherwise empty (fallow) field can out-compete weeds that may grow up later in the year, and they can prevent soil erosion from being blown or washed away (taking the nutrients with it).  For our project, we wanted to know how different cover crop species affect the soil microbial diversity, reduce weeds, put nutrients back into soil, and improve the production of our crop.

We designed this project in conjunction with the Montana Organic Association, the Organic Advisory and Research Council, and Montana organic wheat farmers who wanted research done on specific cover crops that they might use, in order to create a portfolio of cover crops that each farmer could use in specific situations.  As these organizations comprise producers from across the state, our research team was able to get perspective on which cover crops are being used already, what growing conditions they will and won’t work in (as much of Montana is extremely dry), and what production challenges growers face inherent to planting, managing, and harvesting different plant types.

Drafting Your Team

When you assemble a research team, you want to choose Project Directors who have different experiences and focuses and who will oversee different parts of the project.  A well-crafted research team can bring their respective expertise to bear in designing a large and multi-faceted project.  For our grant, I am the co-PD representing the microbial ecology and plant-microbe interaction facet, about a third of the scope of the grant.  We will also be investigating these interactions under field settings, which requires a crop production and agroecology background, as well as expanding the MSU field days to include organic-specific workshops and webinars, which requires an extension specialty.

Because grant project teams are made up of researchers with their own projects and goals, in addition to providing valuable perspective they may also change the scope or design of your project.  This can be extremely beneficial early on in the grant-writing phase, especially as you may not have considered the limitations of your study, or your goals are too unambitious or too lofty.  For example, the cover crop species you want to test may not grow well under dry Montana conditions, do you have a back-up plan?  However, as the submission deadline looms larger, changing the focus of your study can cost you precious writing time.  Working in a research team requires a high degree of organization, a flair for communication, and an ability to work flexibly with others.

Identifying the research question

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All grants center around a Project Narrative, and funding agencies will provide detailed instructions on how to format your project grant.  Pay strict attention- in very competitive pools your grant can be flagged or rejected for not having the appropriate file names or section headers.  The Narrative gives introductory background on your topic that details the research that has previously been published.  Ideally, it also includes related studies that you and your team have published, and/or preliminary data from projects you are still working on.  The aim is to provide a reasoned argument that you have correctly identified a problem, and that your project will fill in the knowledge gaps to work towards a solution.  Grant panels are made up of researchers in a related field, but they may not be intimately aware of your type of research.  So, you need to be very specific in explaining  your reasoning for doing this study.  If your justification seems weak, your project may be designated as “low priority” work and won’t get funded.

In our case, cover crops have been used by farmers already, but not much basic research has been done on the impacts of picking one species over another to plant.  Thus, when cover crops fail, it may be unclear if it was because of unfavorable weather, because the previous crop influenced the soil in ways which were detrimental to your new crop, because you seeded your crop too sparsely and weeds were able to sneak in and out-compete, because you seeded too densely and your crop was competing with itself, or something else entirely.

You also need to identify the specific benefits of your project.  Will you answer questions? Will you create a new product for research or commercial use?  Will organic producers be able to use what you have learned to improve their farm production?  Will you teach students?  When you are identifying a need for knowledge and describing who or what will benefit from this study, you need to identify “stakeholders”.  These are people who are interested in your work, not people who are directly financially invested.  For us, our stakeholders are organic wheat farmers in Montana and the Northern Great Plains who want to integrate cover crops into their farming as an organic and sustainable way to improve crops and reduce environmental impact.  Not only did our stakeholders directly inform our project design, but we will be working closely with them to host Field Day workshops, film informative webinars, and disseminate our results and recommendations to producers.

Crafting Your Experimental Plan

Once you have identified a problem or research question, you need to explain exactly how you will answer it.  For experiments in the laboratory or field, you need to be incredibly specific about your design.  How many samples will you take and when?  Will you have biological replicates?  Biological replicates are identical treatments on multiple individual organisms (like growing a single cover crop species in four different pots) to help you differentiate if the results you see are because of variation in how the individual grows or because of the treatment you used.  Do you have technical replicates?  Technical replication is when you analyze the same sample multiple times, like sequencing it twice to make sure that your technology creates reproducible results.  Will you collect samples which will provide the right type of information to answer your question?  Do your collection methods prevent sample deterioration, and how long will you keep your samples in case you need to repeat a test?

In addition to describing exactly what you will do, you need to explain what might go wrong and how you will deal with that.  This is called the Pitfalls and Limitations section.  Because basic research needs to be done in controlled environments, your study may be limited by a “laboratory effect”: plants grown in a greenhouse will develop differently than they will in a field.  Or, you might not be able to afford the gold-standard of data analysis (RNA sequencing of the transcriptome still costs hundreds of dollars per sample and we anticipate over 1,200 samples from this project) so you need to justify how other methods will still answer the question.

Supporting Documents

Even after explaining your research question in the Narrative and your design in the Methods sections, your grant-writing work is still far from complete.  You will need to list all of the Equipment and research Facilities currently available to you to prove that your team can physically perform the experiment.  If you will have graduate students, you need a Mentoring Plan to describe how the research team will train and develop the career of said student.  If you will be working with people outside of the research team, you will need Letters of Support to show that your collaborators are aware of the project and have agreed to work with you, or that you have involved your stakeholders and they support your work.  I was delighted by the enthusiasm shown towards this project by Montana organic producers and their willingness to write us letters of support with only a few days’ notice!  You’ll also need a detailed timeline and plan for disseminating your results to make sure that you can meet project goals and inform your stakeholders.

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Poster presentation at ASM 2016.

Perhaps the most difficult accessory document is the Budget, for which you must price out almost all the items you will be spending money on.  Salary, benefits (ex. health insurance), tuition assistance, travel to scientific conferences, journal publication costs, travel to your research locations, research materials (ex. seeds, collection tubes, gloves, etc.), cost to analyze samples (ex. cost of sequencing or soil nutrient chemical analysis) cost to produce webinars, and every other large item must be priced out for each year of the grant.  The Budget Narrative goes along with that, where you explain why you are requesting the dollar amount for each category and show that you have priced them out properly.  For large pieces of equipment, you may need to include quotes from companies, or for travel to scientific conferences you may need airline and hotel prices to justify the costs.

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On top of what you need to complete the study, called Direct Costs, you also need to request money for Indirect Costs.  This is overhead that is paid to the institution that you will be working at to pay for the electricity, water, heating, building space, building security, or other utilities that you will use, as well as for the administrative support staff at the institution. Since nearly all grants are submitted through an organization (like universities), instead of as an individual, the university will handle the money and do all the accounting for you. Indirect costs pay for vital research support, but they run between 10-44% of the dollar amount that you ask for depending on the type of grant and institution, potentially creating a hefty financial burden that dramatically reduces the available funding for the project.  On a $100,000 grant, you may find yourself paying $44,000 of that directly to the university.

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Draft Twice, Submit Once

The Budget is by far the most difficult piece to put together, because the amount of money you have available for different experiments will determine how many, how large, and how intensive they are.  Often, specific methods or whole experiments are redesigned multiple times to fit within the financial constraints you have.  If you factor in the experimental design changes that all your co-PDs are making on the fly, having to balance the budget and reconstruct your narrative on an hourly basis to reflect these changes, and the knowledge that some grants only fund 6-8 projects a year and if you miss this opportunity you may not have future salary to continue working at your job, it’s easy to see why so many researchers find Grant Season to be extremely stressful.

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