2009-2010 Topics Course Offerings

Thank you to all of the faculty who have offered to teach the following Topics Courses this academic year:

Fall 2009

• Topics in marine mammal science (Tyack et al.)
• Adaptive dynamics and evolutionary explanation (Caswell)
• Functional analysis of microbial communities (Mincer, Sievert)

Spring 2010

• Algal genomics (Dyhrman)
• Oceans and human health (Gast, Moore)
• Evolution (Shank)

Please contact the instructors of the Fall courses soon if you plan to take their course. This will help them gauge interest and allow them, to the extent possible, to work out any scheduling issues.

Comprehensive Exam Complete (Phew!)

Congratulations to about-to-be-third-year students Ann Allen, Jamie Becker, Elizabeth Halliday, Kathryn Kauffman, Meredith White, and Maya Yamato. They've all just passed their qualifying exam with flying colors. Here's the exam they took. [I've omitted the questions that were written for individual students by their advisors.]

Joint Program External Review

The External Review Committee for the Joint Program has now completed their visit. Thank you to all who participated by providing me with data or meeting with the committee.

In preparation for the review, Jim Price prepared an overview of the Joint Program to provide some background for the Committee. I thought this document might be interesting (maybe even useful) for everyone, but especially for those of you students and staff who are new to the institution. Here it is.

I've also posted the presentation that I gave to the Committee here. [See if you can catch the embarrassing typo!] Without the narrative to go along with the slides some of them may not seem to have much context. I'll do my best to answer any questions you might have.

During the course of the review, it became clear to me that we (the WHOI Biology Department) do not have a shared vision of what the Joint Program in Biological Oceanography is, and what it should be. I hope we can have a discussion soon after we have the Review Committee's report.

Microbial sequence data workshop

The Center for Microbial Oceanography: Research and Education (C-MORE) is offering a workshop on the phylogenetic analyses of nucleotide sequences from microorganisms.  The workshop will be held July 29 – 30, 2009, at WHOI.  For more information follow this link: /WHOI_ARB_workshop.pdf.

New Handbook

A new version of the Handbook for Students and Advisors in the MIT/WHOI Joint Program in Biological Oceanography has been approved by JCBO. (There is a link to it in the "Links" section at right). 

Important updates include:

• changes to course requirements (which have been in effect for 2 years now);
• a description of the new comprehensive exam structure;
• links to Joint Program documents and web pages;
• extension request deadlines.

This new version represents a relatively major revision.  I strongly encourage all students and advisors to read it.  If you find that something is missing, confusing, or incorrect.  Please let me know. 

Updates

It has been too long since my last post.  My apologies. Since admissions season ended, time seems to have gotten away from me! So, here's an update on various topics:

• Admissions: The rate of application to the Joint Program in Biological Oceanography continues to increase.  This year we had nearly 100 applicants.  From those candidates we admitted seven; of those four accepted.  They are: Amalia Aruda (to be advised by Ann Tarrant), Santiago Herrera (to be advised by Tim Shank), Nicholas Macfarlane (to be advised by Peter Tyack), and Kristen Hunter-Cevera (to be advised by Heidi Sosik and me). Nicholas Macfarlane deferred his enrollment until 2010.  Skylar Bayer (to be advised by Lauren Mullineaux) was admitted in 2008, and will be enrolling this year, bringing the size of the entering class of 2009 to four.

• Mentoring:  I have received a few receipts for spring lunches between students and their peer mentors.  If you haven't had your lunch yet, please get together with your mentor soon.  (Remember the $25 limit.)  Also, I'll be looking for four new post-generals mentors for the incoming class.

• External Review: Once every five years the Joint Program undergoes a review by an external committee.  The next review will take place in June.  I'll hold a meeting with the students soon to find out if there is anything of which they think we should make the committee aware.  I hope to hear the opinions of the faculty at an upcoming Scientific Staff meeting.   I welcome any thoughts from all of you.

• Topics Courses:  I recently mailed a solicitation for 2009-2010 Topics Course proposals to the Biology Department Scientific Staff and others.  Students, this is your opportunity to recruit someone to organize a Topics Course on a subject about which you'd like to learn more.  

Space for Biological Oceanography Students at EAPS

For students whose advisors are in Woods Hole, the lack of quality work space at MIT has long been a source of irritation. Now, thanks to the efforts of JCBO member Dianne Newmann, and to the generosity of the department of Earth, Atmospheric and Planetary Sciences, that should no longer be a problem.

EAPS has agreed to provide desk space for JP Biology students who don't have an advisor at MIT. Here are the ground rules:

• Students who are in residence at MIT will be offered a desk, but the offer is conditional upon them actually using it and will be withdrawn if the desk isn't used on a regular basis.
  
  
• Students who are commuting from WHOI will be offered a desk or group of desks to share on days when they are up here for classes. That probably means that they can have a locking drawer to store things, but they will share the keys with one or more other commuter students.

• This offer applies for now and should be reconsidered as Shuhei Ono's and Tanja Bosak's groups grow.

Students should express their interest (and true need) for desks to Alla Skorokhod, who will consult with the E25 faculty to figure out the best plan.

Thanks again to Shuhei Ono, Tanja Bosak, Roger Summons, Ed Boyle, and Maria Zuber for helping. 

Biology Department Collaboration Graph

At a recent scientific staff meeting, I made a short presentation about the way we collaborate with each other in the Biology Department at WHOI. There seemed to be some interest in having some of the figures posted, and this blog seems as good a place as any. So, here they are.

My presentation focussed on the scientific staff collaboration graph. The image above is a picture of the collaboration graph that I constructed using data from curricula vitae submitted in October 2008.  Each of the 29 dots in the picture represents one person, either a member of the scientific staff or senior research specialist. If two scientists have coauthored a peer-reviewed publication, their dots are connected by a line. I'll call two scientist who are connected in this way "collaborators." (Of course the forms of collaboration are multifarious, and many significant interactions between scientists are obscured when collaboration is equated with coauthorship, but I had to start somewhere!)  In mathematical graph theory, the dots are called "vertices" and the lines are called "edges."  

The circular representation of the graph above masks some of its structure. It also makes it impossible to tell who is who! So here is another representation, with the vertices labelled:

Click on the image to enlarge it; you still might need a magnifying glass.

A collaboration graph like this is a kind of "social network." Social scientists specializing in organizational behavior have been studying how the structure of an organization's social network affects both its effectiveness as a whole and the social capital---roughly speaking, the benefits that accrue as a result of holding a particular location in the graph---of its members. (Burt [2000] has written an interesting review paper on the subject.)  One purpose of my presentation was to see if we could use some of the ideas in social network theory to help us think about the kinds of people we want to hire into the department.   

Another purpose was to offer a snapshot of the state of collaboration in the department. To that end, I showed some basic properties and descriptive statistics of the Biology Department collaboration graph. Some of these I found surprising:

• There are 43 edges in the graph.
• The graph is connected; i.e., you can find a path from any vertex to any other vertex by traversing edges of the graph. Put another way, you can connect any two scientists in the graph by an unbroken chain of coauthored publications.
• The diameter of the graph---the number of edges that separate the two scientists who are furthest apart (McDowell and Tyack)---is 11.
• Most of the scientists (20) have 3 or fewer collaborators in the department.  One scientist (Weibe) has 7 collaborators.
• One can weight the edges of the graph by the number papers upon which the two collaborators appear as coauthors. Of the 43 edges, a large majority (31) have weight less than or equal to 3. The strongest collaborations are Olson-Sosik (13 papers), Caswell-Neubert (14 papers), Davis-Gallager and Moore-Stegeman (21 papers) and Hahn-Stegeman (27 papers).
• Finally, one can break the graph into "communities," or groups of vertices such that the number of links within the group is higher than the number between the groups. (The detection of communities in large graphs is a mathematical challenge.  Santo Fortunato has given a fascinating lecture on the subject. Ok, maybe it's just fascinating to me.) The weighted version of our collaboration graph turns out to have statistically significant community structure. Here's a picture with the nodes color-coded by community:

Make what you will of the graphs and statistics.  Here's what I think: the state of collaboration in the department is pretty darn good, but could be better. In particular, it would be really interesting to see what might come from collaboration between remotely connected parts of the graph.  As John Stuart Mill put it in his Principles of Political Economy (1891):

It is hardly possible to overrate the value … of placing human beings in contact with persons dissimilar to themselves, and with modes of thought and action unlike those with which they are familiar.  Such communication has always been, and is peculiarly in the present age, one of the primary sources of progress.

2009 Admissions Schedule

Lauren Mullineaux, Ann Tarrant and I have begun reading the applications of prospective Joint Program Biology students.  The number of applications to the Joint Program overall is at a record high this year, and my preliminary assessment is that we have another strong field of applicants in biology.  

Here is the admissions schedule (please mark your calendars accordingly):

• Jan 14 - Applications available for review
• Feb 3 - WHOI Biology Admissions Committee Meeting (to create our short-ish list)
• Feb 5 (9 am)- Biology Department Admissions Meeting
• Feb 5 - Short list due to Academic Programs office
• Feb 12 - WHOI Admissions Advisory Committee "Pizza" Meeting
• Feb 20 - JCBO Admissions Meeting 
• Feb 23 - Joint Program Committee Meeting (final admission decisions made)
• Feb 23 - Begin notifying accepted candidates
• Mar 9-10 - Open House

New Topics Course (Spring '09)

Mike Fogarty, a scientist at the National Marine Fisheries Service, and an adjunct member of the WHOI Biology Department, will be offering a special Topics Course this spring.   Here is a brief description of the course, entitled "Marine Ecosystem Based Management: From Vision to Implementation."

This course will cover current developments in the formulation and implementation of Marine Ecosystem-Based Management. The format will include guest lectures from specialists in marine EBM and student-led overviews and  discussion of seminal papers in the field. Topics to be covered will be the general framework for marine ecosystem-based management in the United States as articulated in the Report of the U.S. Commission on Ocean Policy and related initiatives, international developments and perspectives on this topic,  overviews of the status of marine ecosystems on the global, national, and local scales, governance structures, and management tools and options including use of marine protected areas as a conservation tool.  These issues will be placed in the context of  evolving perspectives on environmental and fisheries management. 

Mike has said he would welcome faculty participation in the course. "One motivation I have for suggesting the course is to forge a stronger relationship with WHOI as we move towards an ecosystem approach to management on the Northeast Continental Shelf."

Here is a syllabus.

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?