New Faces

The first-year students will be beginning their annual migration from Cambridge to Woods Hole soon.  

Li Ling Hamady earned her undergraduate degree at UC Santa Barbara. She will be studying with Simon Thorrold.

Abigail Heithoff hails from The College of St. Catherine (in St. Paul, MN) and will be working with Sonya Dyhrman.

Holly Moeller was an undergraduate at Rutgers University;  Scott Doney, in the Chemistry Department, is her advisor.

If you see Li Ling, Abigail, or Holly around town, please introduce yourself to these newest biology students and welcome them to Woods Hole.

Student Oceanus articles

This past summer, 14 JP students took the course How not to write for peer-reviewed journals: talking to everyone else.  The course, taught by Chris Reddy (Chemistry) and Lonny Lippsett (managing editor of Oceanus), aimed to teach the students "how to write an article related to [their] research (or other topics in marine science) geared to non-scientist audiences and to develop engaging graphics to accompany it." Funding for the course came from the Henry L. and Grace Doherty Professorship in Oceanography. 

A unique aspect of the course was that it paired students with professional science journalists. These journalists helped the students edit their final projects, many of which have now been published online in Oceanus. Among these are articles by biology students Elizabeth Haliday, Kelton McMahon, Christine Mingione, and Kristen Whalen. The pieces by Elizabeth and Christine have also appeared in the Cape Cod Times. Annette Hynes has an article in preparation. Eventually, all of the articles will be collected into a complete Oceanus issue.

Update (Dec. 4, 2008): Annette Hynes' article has now been posted on the Oceanus website.

Discretionary Funds

Each year, for at least as long as I've been the Education Coordinator, the Chair of the Biology Department has set aside a small portion of her discretionary budget to help pay for student-related expenses. This year that portion amounted to $7,500. (Thanks Judy!) 

I've mostly been using the money to help support student travel to conferences, workshops and courses.  I've also been using it to pay for the lunches that are part of the peer mentorship program. But these are not the only things that the money could be used for. Publication costs, small equipment, supplies, etc. are reasonable requests.  

There is still money in the account for this year. To request the money, the student should send a memo to me, along with a supporting memo from the advisor.

Time to Degree

I've been meeting with students who are entering their 5th year in the program over the past month or so.   One purpose of these meeting is to keep JCBO informed about student progress so as to avoid surprises at the annual August review.  I hope these meetings will also give the students an opportunity to discuss anything else that may be on their minds as they begin to think about what comes after graduate school.

Another purpose of theses meetings is to help students stay on track to finish their degree in a timely fashion.  As many of you know,  JCBO has been trying to shorten the time to degree for Biological Oceanography Ph.D. students.  Currently, the median time it takes a student to complete his or her degree from the time that they first enroll is about 5.8 years.  

I won't presume to speak for the rest of the Committee, but I think we need to keep an eye on the time to degree for a number of reasons.  First, the longer a student stays in the program, the more likely significant life events are to occur: students get married, have children, have to deal with "two-body problems", etc., just like faculty do.  These are, of course, all good things---but they do make earning a Ph.D. a bit more difficult.

Second, the longer that a student takes to complete the degree the more likely they are to require financial support from WHOI.  This means less support for other education programs (e.g. Postdoctoral Fellows) and less money that can be used to admit new students.

Finally, time-to-degree is a statistic that prospective students care about.  (I had one prospective JP student ask me about it just today.) They now also have access to the data. Check out the website PhDs.org, for example.  Students can get data on all kinds of statistics, including time-to-degree, to help them rank graduate programs in the ocean sciences (and many other fields).  There they will find that students in the Joint Program (all disciplines) take 5.7 years to finish, as compared to their colleagues at Florida State (5.2 y), Scripps (6.2 y), URI (6.2 y),  Oregon State (6.7 y), or U. of Washington (6.7 y).

I've just returned from Cambridge, where we celebrated the 40th anniversary of the Joint Program.   We heard lectures from Joint Program alumni, many of whom talked about their interdisciplinary research.  

One thing about the lectures sticks out to me: with one exception, they were about biology or were biologically motivated.  It really is a good time to be a biologist!

Dianne Newman added to JCBO

Prof. Dianne Newman, the Wilson Professor of Biology and Geobiology  in the Departments of Biology and Earth and Planetary Science at MIT, and Howard Hughes Medical Institute Investigator, will be joining JCBO effective October 1, 2008. She replaces Jonathan King, who has been the Biology Department's representative for many years.  Please take the time to drop a note to Jon King, to thank him for his valuable service.

From Prof. Newman's website:

Our laboratory is interested in the co-evolution of life and Earth. Specifically, we take an interdisciplinary approach to studying the molecular mechanisms that underlie putatively ancient forms of metabolism. By understanding the way extant organisms function at the molecular level, we hope eventually to gain insights into the evolution of ancient metabolic and biomineralization pathways, interpret the chemical signatures of early life found in the geologic record, and understand how multicellular bacterial communities survive in the context of anaerobic infection.

Prof. Newman will be visiting the WHOI on Nov. 20, 2008 to give the Biology Department seminar.  I'll arrange for lunch with the graduate students.  Let's welcome Dianne to the Joint Program by turning out in large numbers!

Exam Prep Help

As I mentioned earlier, second-year students are starting to study for the comprehensive exam. To help them, I've asked the scientific staff to contribute to a list of papers, books, and other resources that they think are important for the students to be familiar with.  I'll post it here when it's complete.

Now, I don't think anyone on the scientific staff has actually taken the comprehensive exam (at least not in its current form).  But you, post-generals students, you have!  Please help your fellow students by commenting on this post and identifying the papers, books, web pages, etc., that you found most helpful while studying for the comprehensive exam.  I'm sure the second-year students will appreciate your help, and I'll bet the scientific staff will discover something new too.

New JCBO Chair

Effective immediately, the new chair of JCBO is WHOI Senior Scientist Simon Thorrold (pictured here).  All requests for extensions, course substitutions, etc., should be sent to him. Simon is replacing Ed DeLong (MIT, CEE) who has done a great job leading the Joint Program in Biological Oceanography during the past three years.  

Here's a brief biography of our new chair, clipped from a 2004 Oceanus article:

Born in New Zealand, Simon Thorrold received his B.S. from the University of Auckland, and Ph.D. from James Cook University, North Queensland, Australia.  He traveled far across the Pacific and North America, to the Caribbean Marine Research Center and Old Dominion University, Virginia.  He came to WHOI in 2001... Using geochemical markers, he traces dispersal, migration, and population dynamics of marine invertebrates and fish... With much of his work in the South Pacific and Caribbean, Simon has been on many cruises, logging 1000 hours of scuba diving and 800 hours in tropical environs.

Please join me in thanking both Ed DeLong for his valuable service to the Joint Program and Simon Thorrold for agreeing to take the helm.

Comprehensive Exam

Students in the entering class of 2007 are about to embark on what may be one of the most intense, stressful and, ultimately, rewarding experiences during their graduate studies: preparing for the comprehensive exam.  

To help them study, and to help the faculty evaluate the degree of difficulty of the exam over the past years, I've posted an archive (/Comprehesive_Exam_Archive.pdf) of all the exams between 2000 and 2007.  (I'll update the file to include the 2008 exams soon.) 

Interdisciplinary Training

There has been some discussion lately, particularly among the Education Coordinators and the Academic Programs Office, about raising the visibility of "interdisciplinary science" on our web sites.  Apparently, the possibility of "interdisciplinary" research is an important factor for many applicants to the Joint Program who are deciding between graduate schools. 

As someone with a Ph.D. in applied mathematics, working as a tenured scientist in a biology department, I always thought I had a pretty good understanding of "inter-", "cross-", "multi-", and even "trans-disciplinary" science.  And frankly, I've always been skeptical about the wisdom of formal training of graduate students in any area that needs a hyphen.  I've worried that students need to find jobs and that, except for at a few places like WHOI, interdisciplinary training puts them at a disadvantage.  

But, after reading this fun little editorial piece by Sean Eddy, I'm beginning to reconsider. Maybe we need to train students in "ante-disciplinary" science, "the science that precedes the organization of new disciplines, the Wild West frontier stage that comes before the law arrives." But how would we do that? Any ideas?

Journal Selection

Jim Yoder sent a message to all Joint Program students and WHOI Postdocs encouraging them to use the Agreement to Extend Author's Rights when signing copyright forms for journals. When signed, this document (on the MBL/WHOI website) gives "authors and their employing institutions non-exclusive rights to use, distribute, and reproduce material in electronic digital or print form in activities connected with the author's academic and professional activities."  I always use the form myself, and have never had the publisher disagree.

Of course, copyright policies are only one criterion upon which to base a decision about where to submit a manuscript.  (See, for example, Satyanarayana 2003 or Thompson 2007).  If my own experience is common, scientists struggle with the decision all the time.  Do I choose a prestigious journal, a journal with a short time to publication, a society-sponsored journal, or one with "open access?"   And, since rankings can change over time (see the cool movies at eigenfactor.org) how is one to choose? But, at last, the job has been automated!  Jane (the Journal/Author Name Estimator), can do it for you.  Enter your abstract and click the "find journals" button: up pops a list of best matching journals (from Medline) along with some measure of "confidence"  and "article influence." (I haven't figured out what these mean yet.)  

Better still, those of you who are on the editorial boards of journals know how hard it can be to find appropriate reviewers.  Jane can help with that too!  Cut and paste in the abstract, click on "find authors" and up pops a list along with email addresses.   Testing it out with a few of my own abstracts suggests that it works pretty darn well.

Give it a try---but be warned: it's addictive. [Thanks a lot, Hal Caswell, for pointing Jane out to me.]

Mentoring

In reponse to student feedback (and with funding from the Department Chair), I've set up an informal peer mentoring program. First and second year students have been matched up with post-generals students. They'll be reimbursed for a lunch meeting twice a year. I hope that this will provide new students with an additional resource to help them navigate the Joint Program, life in Cambridge and/or Woods Hole, etc. Special thanks to Colleen Petrik for making the matches and to the students who have volunteered to be mentors!

This made me think a little about the role of the Ph.D. advisor as a mentor. It seems to me that some of the most important information advisors convey to their students has nothing to do with the facts, theories and methods of their scientific disciplines.  Rather, it is the example we set as role models.  I know I still ask myself from time to time, "What would my adviser do?"

The handbook, Adviser, Teacher, Role Model, Friend: On Being a Mentor to Students in Science and Engineering (National Academies Press, 1997), puts it this way:

The sum of all those activities-of all your actions as a mentor-is what students take with them after graduation. The image of you as a person will last longer than your words or professional achievements. The power and value of the image will depend on the efforts you have made in building honesty, trust, and good communication throughout your mentoring relationship.

The handbook is a worthwhile read for both advisors and students.

2008-2009 Topics Courses

The topics courses currently scheduled for the 2008-2009 academic year are:

Autumn

• Tarrant, Pineda, Thorrold: Biology and Ecology of Coral Reefs
• Gast:  Oceans and Human Health

Spring

• Dyhrman: Algal Genomics

In addition to these courses, other courses that have been used as topics course substitutions being offered include:

Autumn

• Hahn, Kurtz: Science and Communication 

Spring

• Caswell, Neubert: Introduction to Mathematical Ecology

Times and meeting places for the autumn will be announced by the Academic Programs Office soon. 

There is still time (and room in the budget!) to try to persuade some faculty member to offer a topic course in the spring.  Is there some topic about which you are especially curious?  This is a great opportunity!  Ask and ye shall receive... probably.

Determining Authorship

I recently attended a workshop on ethical conduct in science for WHOI's summer student fellows. It made me think a little bit about authorship, and what guidelines are available for scientists to help them determine who should be included as an author. 

Many universities have official policies regarding authorship. The policies for the Harvard Medical School, Michigan State University and Washington University in St. Louis are typical and closely follow the guidelines adopted by the Institute of Electrical and Electronics Engineers (IEEE) and by the International Committee of Medical Journal Editors. Finally, Kathy Barker published this guide aimed at young scientists in Science Careers.

Most of the guidelines require that each author significantly contributed to conducting the science and drafted or revised the manuscript and approved the final version.  The Journal of the American Medical Association requires all authors to fill out a checklist to certify that they qualify as an author. 

Do you think it would be helpful for WHOI to have an official policy?

IMU announces Citation Statistics report

As professional scientists (or soon to be professional scientists), part of our job is to assess our colleagues' work.  Often these assessments are associated with decisions about promotion or tenure.  Valuing a scientist's contributions can be tricky, especially when you do not share his or her field of specialization. It's tempting to turn to simple bibliometrics---citation data and the statistics derived from them.

The International Mathematical Union has recently released a report about the uses and misuses of bibliometrics. Applying these metrics (e.g., impact factors) to rank papers, journals, and individual scientists is problematic at best.   At worst, it's misleading. 

In addition to making these points quite convincingly, the report includes some fascinating graphs.  Consider, for example, the graph of the average number of citations per article for various disciplines.  What do you think this implies for impact factors?