Thank You

As I recover from Thanksgiving overindulgence, I'd like to take a few moments to thank all of the people who have helped to keep the Biology education programs running this year. Had I compiled this list last year many of the names would have been the same, but many would have been different too. It really is a group effort. So...

Thank you to the staff of the Academic Programs Office at WHOI, particularly Christine Charette, Marsha Gomes, and Julia Westwater, and to Ronni Schwartz at MIT, who keep the gears of the program well-oiled. Their quick, pleasant, and affirmative responses to my frequent requests for help make my job much easier.

Thank you to the members of JCBO---Ed DeLong, Dianne Newman, Martin Polz, Heidi Sosik and Simon Thorrold---who work hard to make sure that all the students in Biological Oceanography have the opportunity to complete their Ph.D. and flourish as independent scientists. (Students, these people really do "have your back.")

Thank you to Lauren Mullineaux and Ann Tarant, who last year as the members of the Admissions Committee read through many (many) files of worthy applicants, saw the best in them all, and helped JCBO make very tough decisions. I also thank them for agreeing to help again this year!

Thank you to Sonya Dyhrman and Gareth Lawson for their service on the Summer Student Fellowship Admissions Committee and Becky Gast for her service on the Postdoctoral Scholar Committee. There are so many good applicants for both programs, and so few fellowships.

Thank you to Mark Baumgartner, Hal Caswell, Mark Hahn, Mike Fogarty, Darlene Ketten, Tracy Mincer, Michael Moore, Lauren Mullineaux, Jesus Pineda, Peter Tyack, Simon Thorrold, Laela Sayigh, and Stefan Sievert, for teaching courses this past year.

Thank you to the 2009 Comprehensive Exam Committee, Cabell Davis, Stefan Sievert, Ann Tarant, and Janelle Thompson, and to all who contributed questions. It's not easy to write challenging yet fair exam questions, but they seem to do it.

Thanks again to Shuhei Ono, Tanja Bosak, Roger Summons, Ed Boyle, and Maria Zuber for finding desk space for our students over in EAPS.

I hope I haven't forgotten anyone; my apologies in advance if I have. I hope you all had a happy Thanksgiving. Hope to see you at the Holiday Party!

Student Accomplishments

Many of our students are recognized for their scientific ideas and accomplishments. We celebrate these in our individual labs, but I think that many of us are unaware of what the students in other labs have achieved. (I certainly was.) Here's a sample:

Michael Brosnahan, who is advised by Don Anderson, won an Outstanding Student Poster Award at the 2009 Gordon Research Conference on Mycotoxins and Phycotoxins. He was also asked to present a "Hot Topics" seminar.

Carter Esch won a North Pacific Research Board Graduate Student Research award to fund passive acoustic monitoring work she will be doing in the Bering Strait. Carter is advised by Mark Baumgartner.

Kelton McMahon won the Sally Richardson Award for the best student presentation at the 33rd Annual Larval Fish Conference. He also won the best student paper award at the 4th International Otolith Symposium for his paper “Stable Carbon Isotope Analysis of Amino Acids in Otolith Protein: A New Tool for Tracking Fish Movement” (M. Fogel, T. Elsdon, I. Mataeo, and S. Thorrold coauthors). Kelton is advised by Simon Thorrold.

Congratulations to Mike, Carter, and Kelton. If you know of any accomplishments of other students, please let me know so that I can properly announce their achievements here.

Old Exams Posted

I found a pile of old comprehensive exams on my desk. (Sometimes things get lost there.) I've posted them in the "Links" section. They come from various years between 1988 and 1996, and include at least one exam from the "megacourse." In addition to their use as fodder for students studying for the comprehensive exam, they also provide a snapshot of what we as a department thought was important for biological oceanographers to know 20 years ago. Is that material still important now? Take a look and decide for yourself.

New Faces

Please welcome the incoming class of 2009:

Amalia Aruda, a former summer student fellow, was an undergraduate at Georgetown University. She will be studying under the supervision of Ann Tarrant.

Skylar Bayer, also an SSF alumna, studied at Brown University as an undergraduate. She will be advised by Lauren Mullineaux.

Kristen Hunter-Cevera earned two bachelor's degrees and her MBA at West Virginia University. Heidi Sosik and I are her co-advisors.

Santiago Herrera-Monroy studied at the Universidad de los Andes, in Colombia. Tim Shank is his advisor.

Amalia, Skylar, Kristen and Santiago are all taking classes up in Cambridge this semester. If you see them there or in Woods Hole, please introduce yourself!

2010 Admissions Schedule

It finally feels like autumn has set in. Before you know it we'll be up to our knees in leaves...and applications to the Joint Program. This year we are trying out an electronic system. Hopefully it will make it easier for potential advisors to review files and will also save on paper. (Keep your fingers crossed.) Thanks in advance to Ann Tarrant and Lauren Mullineaux who will be helping me to evaluate the applications.

Here is this year's admissions schedule (mark your calendars!):

Jan 5: application deadline
Jan 12: application files available to review
Jan 26: first cut (to ~15 files)
Jan 29: Biology Department meeting to match files with advisors

and determine available support and cut list to ~10 files
Feb 11: WHOI Admissions Advisory Committee meeting

(a.k.a. the "pizza meeting")
Feb 12: JCBO meeting
Feb 19: Joint Program Committee meeting (final admissions decisions)
Feb 19: Begin notifying admitted applicants

Open House will be held March 15-16.

Joint Program External Review Report

The report of the external committee that reviewed the Joint Program has arrived. Please read it. Once the semester settles down, I will hold a meeting with the students to see if the report accurately reflects their sentiments. I will also schedule a time to discuss the report with the Scientific Staff. In the meantime, comments are always welcome here on the blog.

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.