PFTF discussion: The Academic Interview Process

The topic at last week's Professors for the Future meeting was the academic interview process! UCD faculty members Julia Simon and Warren Pickett led a great discussion, answering all of our eager questions (and there were indeed many questions).Here are my notes from the meeting, representing a mix of the speakers' slides and other discussion points I jotted down:

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Presenting Yourself

Your apparel:

• Don't stand out because of what you wear - the search committee is not looking for a mannequin
• You should be comfortable in what you wear, and other people should not be made to feel uncomfortable because of what you wear.
• The best scenario: your host should not be able to remember.
• Its about what you know and do, not about what you wear.
• Practices might be different in law school, business, vet school, etc. - Know your discipline and its general practices.

Note: I disagree with some of the above advice. Dressing yourself for an interview is both a skill and an art (and should be highly personalized). A memorable piece of clothing (shoes, scarf, printed skirt) can be a conversation point, so don't feel you need that you have to dress boring to be taken seriously. This topic deserves its own post, but I reccommend you check you this article at Inside HigherEd.

Don't be someone else - be yourself, but be on your "best behavior"

• Be positive, and express enthusiasm about the future and the institution
• Be prepared to ask questions - to learn about the new environment
• Know your viewpoints on the questions of the day (in your discipline)
• Keep a lid on your politics - it will not help, and it might hurt. Don't play stupid, but just put on a tolerant front.

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Structure of the Interview Schedule

• Typically, interviews are a two day campus visit where you meet with the department chair, the dean, and many other people (e.g. half-hour meeting with prospective colleagues).
• Do some homework (IMPORTANT!):
• Learn about your schedule and presentations (even though you might only get it 2 days beforehand)
• Know something about the department and institution
• Know something about several faculty members
• Ask people about their interests, as well as talking about yours.
• Generally be an interesting person to converse with
• Often the search committee is invisible - but they will be paying much more attention than the typical faculty member.
• The most important people you'll meet during your interview are: 
• The faculty in your area of research
• The rest of the faculty 
• The chair (whose job it is to work with you)
• The dean (who improves the faculty, while balancing the budget). Although the faculty vote on who to hire, the dean has to sign off on this decision: so be sure not to rub them the wrong way!
• Be prepared! Understand the needs of the group (e.g. the department) and the reason for the search. Is the search specific, to fill a particular need? Or is it more general: to shore up the group and its teaching needs, to find the "best person at this time?"
• This aspect becomes more important at higher levels of hiring - what is your "vision" (for the group, department, division, college)? What are the existing strengths and imminent challenges?
• Things that you can (should) ask the dean/chair: 
• What is the tenure review process? What is the typical teaching load (and is there a policy for new faculty to have a one-semester reprieve while they adjust to the new job)?
• What is the sabbatical policy? What is the family/childcare policy? - but perhaps consider the kind of institution you're interviewing at before asking these two questions

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Research Presentations

• You will be expected to give one or two talks (and be sure to understand the purpose and audience): 
• one for a "general" audience, colloquium style for all in the department/group
• one or more related to your research specialty - still, do not be specific for these talks. Introduce the field, discuss various viewpoints, finally get to the point(s) you want to convey to the audience. But avoid too many details; let them read your papers.
• Your presentation gives the exceedingly important impression of how well you can get your ideas across - essential for both education and for research, and more generally in interactions with colleagues 
• Caveat: being a good speaker is important; but you don't have to be the best 
• Most important: know your audience and keep them interested

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Your Self-Presentation

• Important: know what your plans and hopes are, and be able to articulate them well and field questions
• Have a well thought-out research plan
• What is the intellectual "hook" that makes you so excited?
• Where will the funding support come from? Do you have experience?
• What broader requirements do you have? Collaborators, travel, seasonal restrictions?
• To what degree are you already connected in the field?
• Education: readiness and aspirations
• What style of teaching is effective in your field and why?
• What new approaches do you find intriguing, exciting?
• You can suggest what courses you'd like to teach, but be careful in case a course is someone's "pet". 
• Good to ask "what are your undergraduates like?" - this is something you'll want to know, but also show that you did your homework.

Examples of what NOT do do or say:

• "I'm enthusiastic about research now. I may go into administration when I get tired of research" (said to a dean)
• Don't paint yourself into a corner by demanding/requesting a larger start-up package than is reasonable. Find out what is customary, perhaps get some input on limitations.
• Don't give the impression you need/deserve special considerations (the process needs to be fair to all)
• Don't be derogatory about planned social events - complaining about restaurants, food, etc.

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Other things to consider

What usually seals the deal: 

• Research Area Fit (you can't control this - this is a search committee decision)

• Whether or not you connect with everyone and can have intellectual discussions during your interview (you can practice and prepare for this)

If you have a phone interview, try to use Skype if at all possible (and remember to look at the camera, and be sure the background is appropriate). Its generally hard to be engaging and sell yourself over a speakerphone.

Be concise in answering questions - aim for a 3 minute answer, then watch for body language and engagement with the person. Your eye contact and body language are also very important - don't look too rigid or too relaxed (no lazing on a sofa).

You'll have to be adaptable for questions about "service" - you can't be sure what they'll ask, and you will have to think on your feet.

Be prepared to defend yourself - search committees may want to challenge candidates. Politely, calmly stand your ground and give good arguments.

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The Bottom Line

The search committee and faculty are a group of individuals, with different opinions and means of evaluation. What works for some may not work for others. Search committee members negotiate with one another and present a recommendation to the faculty, who then vote. 

The above guidelines may be helpful. But the bottom line is, there is no bottom line.

Intra-Genomic Variation in the Ribosomal Repeats of Nematodes

Happy to announce our new paper, published last week in PLoS ONE:

Bik HM, Fournier D, Sung W, Bergeron RD, Thomas WK (2013) Intra-Genomic Variation in the Ribosomal Repeats of Nematodes. PLoS ONE 8(10): e78230. doi:10.1371/journal.pone.0078230

This manuscript was in the works for a while, and was based on undergraduate research carried out by co-author Dave Fournier while he was an undergraduate at UNH. The rationale? To assess the level of variation in rRNA loci within a single nematode genome, as well as between genomes of different nematode species. rRNA is typically present as a repeated, muti-copy locus in eukaryote genomes, which makes it hard (impossible) to correlate gene abundance to organismal abundance in environmental sequencing studies. Unlike bacteria, there is no known correction that we can apply to "normalize" DNA for species with multiple rRNA copies - every species has multiple copies (sometimes into the thousands!) and we know little about the typical ranges of rRNA copy number across different eukaryote groups.

In this manuscript were were asking questions about both rRNA copy number (how many rRNA repeats are present in a genome?) and intragenomic variation (how many of these copies are unique rRNA gene sequences within a genome, and across rRNA variants are there "hotspots" for base polymorphisms?). We wanted to determine if we could spot patterns that govern rRNA copy number and level of intragenomic variation amongst gene copies - taking into account things like genome size and phylogenetic distance.

The result? There doesn't seem to be any pattern determining copy number or intragenomic rRNA variants across species, which kind of makes biodiversity estimates from environmental rRNA studies feel like a shot in the dark. But we DID find some interesting evidence of selection acting on rRNA loci:

By applying the same approach to four C. elegans mutation accumulation lines propagated by repeated bottlenecking for an average of ~400 generations, we find on average a 2-fold increase in repeat copy number (rate of increase in rRNA estimated at 0.0285-0.3414 copies per generation), suggesting that rRNA repeat copy number is subject to selection. Within each Caenorhabditis species, the majority of intragenomic variation found across the rRNA repeat was observed within gene regions (18S, 28S, 5.8S), suggesting that such intragenomic variation is not a product of selection for rRNA coding function.

Divergence and polymorpishm are illustrated in the figure below:

Figure 1. Variation observed in nematode ribosomal arrays. (A) Divergence in rRNA repeats observed between the genomes of C. elegans, C. briggsae, C. japonica, and C. remanei; here, base substitutions are denoted as transitions or transversions, while complex polymorphisms represent any type of insertion, deletion, or inversion event. (B) Polymorphic positions in rRNA repeats observed within the genomes of each Caenorhabditis species. Results suggest that the pattern of intragenomic polymorphisms is unique across repeats within a species, whereas patterns of interspecific divergence reflect a strong signature of natural selection for rRNA function. 

The data on genomic patterns in eukaryotic rRNA is still very preliminary, and this paper is just a starting point. Hopefully this type of work will inspire similar analyses in other groups - we desperately need more knowledge, particularly for non-model organisms.

The Fisher Files - podcast series on academic productivity

Last weekend I took a road trip to LA, and I needed something inspiring to make the 7-hour drive on the CA I-5 less tedious.

I came across The Fisher Files, a fabulous podcast series originally recorded by MIT physicist Peter Fisher (since collated and rescued from internet oblivion by the Foonyor Barzane blog). In addition to the typical career advice (PhD/postdoc/junior faculty), there are some great musings on how to promote personal productivity and efficiency in academic life.

I'm über-organized, so a lot of the advice was reassuring - after listening, I think I seem to be doing things right (organizing my calendar, reviewing/assigning work tasks on a weekly basis, etc.). But it was still great to hear how a senior academic manages his career and work life - I always like to try out new things and pick up tips I might not have thought about. For example:

Fisher argues that meeting should ideally adhere to three rules: 1) Always stick to a one hour timeslot, 2) Always prepare and distribute and agenda, and 3) An effective way for meeting chairs to move on from a discussion is to first summarize peoples' thoughts and ask if there are any final, additional points. If people start to repeat ideas say "we already discussed this" and move on. This can be necessary to cover all agenda items within the allotted time.

For my to-do lists, I've now added a couple subheadings that Fisher suggested - an "agenda" list where I keep track of things I need to discuss with different people (so when they drop by your office, you remember what you need to ask them), and a "waiting on" list where I keep track of outstanding items that require action by others.

So far I've only made it halfway through the podcast series (each topic is about 30 minutes long), but I would definitely recommend it to other researchers!

Fun with Myers-Briggs Assessments!

This week at PFTF we went through results from our Myers-Briggs Type Indicator Assessments, and used our profiles as a discussion point for careers outside academia.

I guess I'm a bit unusual because I've wanted to do biological research since high school, and even way back then I knew I wanted a PhD and a career in academia. I've never deviated (or considered deviating) from this path. But still, I always find these personality assessment tools fun to look at - particularly from a management perspective, so I know what my weak points are when it comes to dealing with employees and colleagues. However, my profiles on these things are never a surprise.

I am an ENTJ according to Myers-Briggs:

Frank, decisive, assume leadership readily. Quickly see illogical and inefficient procedures and policies, develop and implement comprehensive system to solve organizational problems. Enjoy long-term planning and goal setting. Usually well informed, well read, enjoy expanding their knowledge and passing it onto others. Forceful in presenting their ideas.

Yep, the MBTI has me down to a T. Inefficiency drives me insane. I set daily goals every morning, and I'm already filling in iCal events for 2015. The MBTI rated science and law as two of my top recommended career choices, and I was weighing exactly those two options in high school.

Some people in our group expressed skepticism (or resistance) to these type of personality assessments, but I think everyone should complete one at some point to gain some insight on their natural personality tendencies. The results can be eye-opening, particularly if you're looking to make a change or searching for the ideal career path.

We finished up with some recommended external readings:

• The Search Is Over (Chronicle of Higher Ed) - transitioning out of academia
• How to do an Informational Interview (Chronicle of Higher Ed) 
• Do What You Are: Discover the Perfect Career for You Through the Secrets of Personality Type (Amazon.com - book)

Conflicts of interest and the privatization of the public university

Today marked the start of our Ethics and Professional Integrity discussion seminar that I'm taking as part of the Professors for the Future (PFTF) program (well technically it's the second class, but I was in Alaska last week and missed the start of fall quarter). The topic was "Conflicts of interest and the privatization of the public university," and we had two readings:


Kezar, A.J. (2005). Challenges for higher education in serving the public good. In A.J. Kezar, T.C. Chambers, & J.C. Burkhardt (Eds), Higher education for the public good (pp. 23-42). San Francisco: Jossey Bass.

• This was a perspective on the changing nature of Higher Education, where universities have moved from their historical roles as social institutions serving the public good, and towards commercialized ventures with strong links to industry. Our discussion group noted that although some of the evidence were a bit one sided, many of the arguments were spot on: the move towards cost effective lecture-based courses, increasing numbers of part-time and contract faculty, corporate administrative structures, and privatized and commercialized research.
• The one thing this article missed was the impact of technology (not surprising, since today's technological landscape was still very much emerging when the article was published in 2005). Although we also noted that technology can exacerbate some of the problems in Higher Education (e.g. online courses that bring in substantial tuition money, with little student interaction beyond "ticking boxes").

Shamoo, A.E. & Resnik, D.B. (2003). Conflicts of interest and scientific objectivity. Responsible conduct of research (pp. 139-162). Oxford: Oxford University Press.

• We tied this article into the previous reading, basically by arguing that the new landscape of Higher Education is essentially in conflict with itself (the lofty mandate of pure intellectual pursuits vs. the new reality of students as paying customers).
• Our discussion emphasized that conflicts of interest are everywhere, and not necessarily bad. However, it is prudent to be aware of these conflicts and disclose them up front whenever possible. The case studies in this reading focused on COIs in the life sciences, but our group noted that the humanities are just as susceptible (e.g. authoring a textbook and requiring students to buy your textbook for a course).

We discussed how the incentive structure and cutthroat competition in academia can promote certain conflicts of interest. There were several case studies where corporate financial interests (accepting funding from pharmaceutical companies) led to unethical research practices. I also argued that paywalled articles and non-open access data put scientists in conflict with what's fundamentally best for the public good--especially if the research was taxpayer-funded in the first place.

I'm really enjoying this discussion seminar - we have a small, lively group representing both the sciences and humanities, so its been great to hear viewpoints from a diversity of disciplines.

A Quickstart Guide to Navigating University Administration

I'm currently participating in the “Professors for the Future” (PFTF) program at UC Davis for the 2013-14 academic year (more about that here). PFTF is a year-long competitive fellowship program designed to recognize and develop the leadership skills of grad students and postdocs - I was selected after a nomination and application process. The program is pretty intense, and involves all these things: 1) biweekly meetings focused on careers and professional development, 2) A discussion seminar course on "Ethics and Professional Integrity", 3) a "Seminar on College Teaching" course, 4) spring and fall program retreats, and 5) individual projects (read about my project here).

At our fall retreat, Jeff Gibeling (our Dean of Graduate Studies) gave us a great rundown on University Administration. This was extremely useful, and helped clarify all those various titles you always hear being thrown around (vice-chancellor, provost, dean, chair, etc.). In short, the structure of any given university can be summed up by this neat little diagram:

The Board (or Regents in the UC system) is at the top of the administrative hierarchy. Board members are not usually academics, but rather entrepreneurs, businessmen, or people who have political connections (here are the UC system board members). They are selected by the governor for 12-year terms, and these appointments are approved by the academic senate.

The President or Chancellor is one step below, representing the administrative head of a university. The name of this position can be confusing - in the UC system, the President is the system-wide administrative head of all the UCs, while the Chancellor is the administrative head of one UC campus. Other universities may have both positions (President and Chancellor) that serve different functions.
The Provost is the Chancellor's second-in-command, and the chief academic officer of the university.

The right-hand side of the above diagram can be considered the "Executive Branch" of a university, encompassing all the Vice Chancellor and Vice/Associate Provost positions. The name and number of these positions varies across universities, and they may or may not be filled by faculty members (it varies according to the job duties of the specific position).

Below the Provost we come to the Colleges, Schools, and Departments. Departments are the most fundamental structure of a university, groups of Departments together form a School or College. [Note that in at UC Davis, a "School" offers only graduate and professional training, while a "College" offers both undergraduate and graduate training.] Each School/College is headed by a Dean, and each Department in the School/College is headed by a Chair (who reports to their respective school/college Dean). Department Chairs are senior (usually tenured) faculty members: they may be promoted to this position from the pool of faculty members in a department, or occasionally brought in as an external hire. Chairs are in charge of organizing committees, managing departmental budgets, managing the tenure review process, and overseeing the hiring new faculty members.

The left-hand side of the above diagram, the Academic (Faculty) Senate, can be considered the "Legislative Branch" of a university. The Senate is the pool of all junior and senior faculty members from different departments, who are organized into lots of different committees (each with its own chair) and act as a governing body. This is where all your academic "service" obligations come in. Apparently UC Davis has about 30 different committees focused on various issues: the Graduate Council, the Undergraduate Council, Research Committee, Tenure and Promotion Committee, Courses Committee, Academic Freedom Committee, and yes, even a "Committee on Committees" (which appoints members and chairs to other committees).

Finally worth pointing out are Graduate Groups - these are specific, interdisciplinary graduate programs that draw faculty members from different departments. The UC Davis Graduate Group in Ecology, as an example, represents 24 different departments on campus!

This is just a quick (and hopefully useful) overview based on the organization of the UC System, and UC Davis in particular. There can be a lot of variability in administrative structure. However, some things are pretty consistent: for example, you'll always find a Vice Chancellor for Research and a Vice Chancellor for Student Affairs.

Microbial Phylogenies have the *least accessible* data in systematics

This month in PLoS Biology, "Lost Branches on the Tree of Life" gives us a pretty stark overview of data sharing and accessibility in the systematics community. The paper assessed just how many published phylogeny papers also deposited their corresponding sequence alignments, tree files, and program parameters. The grim news:

...only 16.7%, 1,262 from a total of 7,539 publications surveyed, provided accessible alignments/trees (Figures 1 and 2). Our attempts to obtain datasets directly from authors were only 16% successful (61/375; see Table S4), and we estimate that approximately 70% of existing alignments/trees are no longer accessible. Thus, we conclude that most of the underlying sequence alignments and phylogenetic trees produced by the systematic community during the past several decades are essentially lost, accessible only as static figures in a published journal article with no capacity for subsequent manipulation. Furthermore, when data are deposited, they are often incomplete (e.g., what characters were excluded, accepted taxon names; see Text S1 and Figure S1). Our survey of publications that implemented BEAST revealed that only 11 out of 100 (11%) examined studies provided access to the underlying xml input file, which is critical for reproducing BEAST results. Although funding agencies often require all data to be accessible from funded publications, our results reveal this is more the exception than the rule.

What made me cringe even more is that my discipline (microbial systematics - including microbial eukaryotes, bacteria and archaea) are the worst offenders when it comes to data sharing. The green line indicating full data deposition is pretty much flatlining in some years for microbes! (Drew et al. 2013)

I'll be the first to admit that my own data is part of the problem - when I was doing my PhD, no one ever had a conversation with me about data reproducibility and sharing. I made my best effort to publish the supplemental files I thought would be useful, but at that time I wasn't in the loop about scientific reproducibility and best practices for data archiving. For my nematode phylogeny paper in BMC Evoltionary Biology, I did upload the original ARB databases I used to construct and edit the rRNA structural alignments; but in hindsight, this file requires knowledge of the ARB software itself (not an easy package to use), and I didn't even think to publish a FASTA alignment file or a Nexus tree file. Partially this was because my Phylogeny papers involved a multitude of topology tests and I didn't think it was correct to pick just "one tree" to represent my spectrum of results.

I've been thinking about this issue a lot recently, and taking strides to correct my past mistakes. I'm now digging through old PhD files to find my alignments and tree files to contribute a nematode phylogeny for the Open Tree of Life project. I'll also post these data on Figshare so my data will no longer be another "Lost Branch" on the Tree of Life.

Reference:

Drew BT, Gazis R, Cabezas P, Swithers KS, Deng J, Rodriguez R, et al. (2013) Lost Branches on the Tree of Life. PLoS Biology, 11(9):e1001636.