Perspective on developing curricula

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

Organization of materials

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

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

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

Written assignments (when logistically possible)

A stack of papers facedown on a table.

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

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

Red pen.
Photo credit: Merriam-Webster

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

Stacking assignments for improved retention

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

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

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

An inclusive syllabus

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

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

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

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

AVS 590 Syllabus spring 2020

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

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

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

AVS 590 Syllabus spring 2020

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

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

AVS 590 Syllabus spring 2020

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

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

Silhouettes of four people jumping in a dark cave.

AVS 254: Introduction to Animal Microbiomes

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

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

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

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

DNA double helix with dollar signs as a nucleotide.

The cost of scientific publishing

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

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


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

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

Buildings: $1006 APC (always open-access)

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

Indoor Air: $4300 APC for open-access

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

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

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

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

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

Total cost: $21,241


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

It takes a village to write a scientific paper

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

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

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

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

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

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

 

Featured Image Credit: Kriegeskorte, 2012

Finding the write words

Recently, a colleague recommended using Voyant Tools to analyze texts, so I thought I would give it a try.  Language metrics can give a fascinating look into a text, and in this example, into what my most commonly used words are, how verbose I can be, and how diverse my written vocabulary is.  It’s important to note that these metrics are sensitive to citation style, the use of text in legends or tables, and other bits of text in manuscripts or webpages that may get incorporated which aren’t part of the text, strictly speaking.  When possible, I uploaded just the written portion of the manuscript.

My first publication

Insight into the bacterial gut microbiome of the North American moose (Alces alces), was written in 2012 and published in BMC Microbiology, which does not have a word limit.  According to Voyant, the document contains 5,904 total words and 1,489 unique word forms. Vocabulary Density, the ratio of the number of words in the document to the number of unique words in the document, is 0.252.  A lower vocabulary density indicates complex text with lots of unique words, and a higher ratio indicates simpler text with words reused. Average Words Per Sentence is 27.1, and Most frequent words are: rumen (80); otus (68); samples (67);  moose (54); colon (50)..

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My latest first-authored publication

An investigation into rumen fungal and protozoal diversity in three rumen fractions, during high-fiber or grain-induced sub-acute ruminal acidosis conditions, with or without active dry yeast supplementation, was written in 2017 and published in Frontiers in Microbiology, which also doesn’t have a word limit.  For this one, I altered the citation style first.  As Frontiers uses a verbose citation style (Author et al., year), my top words were “et” and “al” in the published version of the paper.  In the modified version, there are 7,580 total words and 2,067 unique word forms. Vocabulary Density: 0.273, Average Words Per Sentence: 12.7, Most frequent words: rumen (111); diversity (69); diet (56); fungal (47); protozoa (46).

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My dissertation

My dissertation, written in 2015, contains 75,859 total words and 8,958 unique word forms. Vocabulary Density: 0.118, Average Words Per Sentence: 12.9, Most frequent words are: rumen (632); moose (411); sequences (323); using (304); samples (284).

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Summary

To look at all my first authored research publications to date, I put all the text from the word documents together, excluding figure and table legends, as well as reference lists. Across these 8 documents, there were 40,860 total words and 5,059 unique word forms, Vocabulary Density: 0.124, Average Words Per Sentence: 26.6, Most frequent words: rumen (304); samples (301); sequences (275); using (265); moose (226).

ishaq all docs
Word cloud from 8 publications.

 

 

Where does the time go?

As we rapidly approach the end of both the fall semester and 2017, it’s a great time to  reflect about the year’s accomplishments (update your C.V.) and look forward to what 2018 will bring (panic about all the things you haven’t finished yet that need to be completed by the end of the year).

Time management is a reoccurring theme in academia, and with so many items on one’s to-do list, it’s not hard to see why.  Everyone has their own advice about how to be more effective; which was the very first meeting in this year’s Faculty Organizing for Success professional development workshop series, which I attended in October.  I compiled some of the suggestions made there, along with advice I’ve picked up over the years, and strategies I use which I’ve found to be effective.

One of the major questions that came up at the FOS meeting was time management in the face of academic duties, namely service.  Academics have a requirement to provide service or outreach to their university, the community, and their field, and as I’ve previously discussed, these amorphous responsibilities can be time-consuming and under-appreciated.  Sometimes, turning off your ringer, closing your email application, or saying “no” isn’t enough or isn’t possible.  So, how can you make the most of your time while navigating the constraints of a fractured schedule?

Lists

  1. I find lists to be extremely helpful in keeping track of everything I need to do, and it really helps me focus on what I need to get done TODAY.  
  2. Lists help me organize my thoughts
    1. by adding notes for each particular item
    2. and ordering the steps I need to take to finish each item.
  3. Being able to cross tasks off a physical list is also a great visual reminder that you are, in fact, being productive.  
  1.  And, at the end of the day, the remaining items form a new list, so I know where to begin tomorrow.  This saves me a lot of time which would otherwise be spent trying to remember where and how I left off.

Calendars

Don’t like lists?  I also heavily rely on my calendar and will schedule appointments for everything, especially the little things that I’m liable to forget, including catching up on emails, lunch, reading articles, writing posts, etc.  I utilize color-coding and multiple calendars within a calendar, like shared calendars from research labs or online applications.  I have learned to schedule small blocks of time after meetings, especially project development or brainstorming meetings, during which I can write notes, look up deadlines, send emails, or any other action items that came up during the meeting while it’s still fresh in my mind.  I even schedule appointments for my personal events, like hiking, movies, or buying cheese at the farmer’s market.  Having them in my calendar keeps me from scheduling work-related things into my personal time.  Academics, myself included, have a habit of working more than 40 hours a week: “Let me just send this email real quick” can easily transform into “Well, there went my Saturday”.

I’ve been known to schedule reminders months or a year in advance, perhaps to catch up with someone about a project, to have a certain portion of a project completed by a soft deadline, or look up a grant RFA that will be made available approximately three months from now.  Making good use of my calendar has been particularly important for tracking my time for reporting (or billing) purposes. BioBE and ESBL use the Intervals tracking program, and it’s much easier to report my time if I have a detailed account of it in my calendar.  Even better- it’s great for retrospective reports:

Screen Shot 2017-11-14 at 11.36.46 AM.png
The categorical break-down of how I have spent my time from June to November.

 

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That time has been used for a number of different projects.

Perhaps the best use of my calendar has been to schedule themed time-blocks spanning several hours, such as “catching up on projects” or “data analysis”, specifically on a shared or public calendar to prevent time fractionation.  These events are marked as tentative, so I can be scheduled during those times as needed, but I find that I get fewer requests for my time when I don’t have unclaimed space on the calendar.  And, I can focus on a specific project for several hours, which I prefer to a “30 min here, 60 min there” approach.  If possible, I also try to concatenate meetings, seminars, training and workshops, or other short but disruptive events.  One or two stand-alone events can be a nice way to break up the day, but too many can fracture my time into small blocks and make it very difficult to effectively perform the research portion of my work which is best accomplished when I can puzzle out problems at my own pace.  So, I categorize the day as “administrative”, “social media“, or “project management”, and spend the day taking care of all the other responsibilities I have that are tangential (but important) to my research.

Emails

Prioritizing my emails with flags is also really helpful, especially if you can color-code by importance.  I get dozens of emails every day, from six different email accounts, but I keep my inboxes to less than 10 items each, almost every day.  I spend a few minutes to prioritize them for later, I archive old emails into other folders for future reference, and I dedicate time to deal with my emails on a daily basis.  I also liberally use the “unsubscribe” link.  

Screen Shot 2017-11-14 at 1.17.49 PM.png
Actual screenshot from one of my inboxes.

Caution: Work Zone Ahead

SantaCruz-CuevaManos-P2210651b.jpg
Cueva de las Manos, Perito Moreno, Argentina.

Academics love to work outside the office- most often because the office is where everyone goes to find you for some reason.  Coffee shops, parks, airports, and homes are popular locations for “writing caves” (I’m writing this from home right now).  Being in a distraction-free, or distraction-specific (i.e. white noise of cafe chatter) location helps me focus on things without interruption.  When I’m analyzing data or writing up results, I have multiple computer application windows open and am collating information from multiple sources, so I need to focus or else I waste a lot of time trying to pick up where I left off after every interruption.

 

Screen Shot 2017-11-22 at 6.09.48 PM.png
Monty Python

When I’m stuck on something, sometimes I’ll take a walk- usually to go get coffee.  Ok, always to go get coffee.  Exercise stimulates blood flow and lattes are full of glucose, so it’s a perfect way for me to recharge.  Often, that change of pace is all I need to accomplish in 2 min what I was struggling to put together earlier.  My best ideas often coalesce while hiking or biking home, so I started taking pens and notepaper with me so I can write them down on the fly before I forget.

When possible, I also try not to force myself to work to continue working on specific things past the point where I can make progress on it (you know, for all those times I’m not up against a deadline- haha).  Of course, this flexibility in my schedule during business hours is a privilege that most people don’t enjoy.  It also takes a great deal of self-motivation to enforce, but it can be very effective for me.  Instead, I set that project aside and  focus on something else entirely.  Often, this leads to procrastinating work with other work, but it’s productive nonetheless.  But for me, it also leads to more effective work-life balance. Late afternoons are not a particularly productive time for me; it’s better if I leave early and go grocery shopping, and then work for a few hours in the evening or on Saturday mornings, when I can get an extremely productive hour or two in after I’ve had time to mull things over.  Having down time built into your day has been shown to improve productivity.

Conversely, when I get new data, start writing a new grant, or acquire a novel task, my interest and enthusiasm are high and I’m tempted to drop everything else to start working on it. Following that passion for a day or a week gives me a great start in which to outline what I’ll do for the next few weeks or months.  Then, as my enthusiasm ebbs, my thoughts wander, and other deadlines become more pressing, I can set it aside and pick that outline up later after I’ve thought it over.  Collectively, these strategies allow me to be productive without reallocating time that I would otherwise use for sleeping, and without racing against the clock to submit something.

Find a system you like and stick to it

Everyone uses different technology and productivity applications, and everyone has a different style of organization, so you may have to try different things to find a method you like.  But once you find something that works for you, stick with it.  Too often I see people abandon a time management strategy because they don’t have time to invest in adapting to it.  Maybe you have several hundred unread emails you don’t want to sort, maybe you are having syncing issues across multiple device operating systems, or maybe you keep forgetting to use your strategy because it hasn’t become habit.  I encourage you to devote time to becoming comfortable with some time management strategy, as I can personally attest that it will pay off later.

Featured Image.

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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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.

My first week at the University of Oregon

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My new work home.

Last week was my first week as a Research Assistant Professor in the Biology and the Built Environment Center (BioBE) at the University of Oregon, and my first full week in Eugene.  Combined with the Energy Studies in Buildings Laboratory, our collaborative team of architects and biologists researches how to make buildings more efficient, sustainable, pleasant, and healthy.

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Delta Ponds, along my new bike route to work.

My first day started auspiciously as I charted a new bike route to work, about 4.5 mi of which is along a path snaking next to the Willamette River.  It goes through several parks, and by a few small lakes and swamps which are home to dozens of species of birds, mammals, amphibians, and reptiles.  I haven’t seen any river otters yet, but I have been keeping a close eye out.

Arriving on campus, most of my first day, and first week, were spent visiting the various places around campus to get myself established as a new employee- obtaining my ID card and email address, filing out paperwork, attending orientation, and finding all the coffee places within walking distance of the building.  ESBL is renovating and expanding its offices across several large, pluripotent rooms to accommodate a growing research team, so I got a brand new standing desk, chair, shelving, and computers (on order), all to my specifications.  The flexibility of working position, screen size, and screen angle provided by my new station are comfortable and great for productivity, and it’s neat to design the new space into offices, meeting tables, and storage which are based on our personalized usage needs and preferences.  And of course, there is plenty of space for all the mementos and science toys I’ve accumulated.

Most importantly, my first week was spent acclimating to my new department and getting up to speed on the ongoing and planned projects.  BioBE and ESBL have dozens on ongoing or planned projects on the built environment, with a combination of building and biology facets.  Over the course of the summer, I’ll be writing several grants and organizing new projects that explore how building use, occupancy, and human habits affect human health and the indoor microbiome, as well as contributing to the BioBE blog,  providing building microbiome posts to Give Me the Short Version, and getting some older projects out for publication.  On top of that, I’m looking forward to exploring the Pacific coast and the Northwestern landscape, and availing myself of the Willamette Valley wine industry.

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Photo Credit: Alen Mahic

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