SEA  Semester®:  Marine  Biodiversity  &  Conservation  

www.sea.edu              Directed  Oceanographic  Research  -­‐  1  

Directed  Oceanographic  Research  XAS  NS  325  (4  credits)    Course  Catalog  Description  (max.  40  words):  Design  and  conduct  original  oceanographic  research.  Collect  data  and  analyze  samples.  Compile  results  in  peer-­‐reviewed  manuscript  format  and  share  during  oral  or  poster  presentation  session.  Emphasis  on  development  of  research  skills  and  written/oral  communication  abilities.    Instructor(s):  Sea  Education  Association  Oceanography  Faculty    Location:  SEA  campus  in  Woods  Hole,  MA  and  at  sea  aboard  an  SEA  sailing  school  vessel.    Prerequisites:    Admission  to  SEA  Semester.  Three  lab  science  courses  (one  at  the  300-­‐level  or  higher)  or  consent  of  instructor.    Course  Philosophy  and  Approach:    This  course  is  part  of  the  suite  of  required  courses  in  the  SEA  Semester:  Marine  Biodiversity  and  Conservation  (MBC)  program.  Collectively,  the  MBC  courses  provide  the  context,  tools,  and  opportunity  for  students  to  make  authentic  contributions  to  the  international  effort  to  protect  the  Sargasso  Sea  ecosystem.  This  course  is  dedicated  to  practical  biodiversity  data  collection  and  dissemination  of  original  scientific  research  results.    

Research  project  proposals  have  been  fully  developed  prior  to  the  start  of  the  sea  component  and  this  course  (see  syllabus  for  Advanced  Topics  in  Biological  Oceanography:  Biodiversity).  At  sea,  students  work  collectively  during  laboratory  watch  to  sample  for  all  projects.  Students  acquire  practical  skills  in  sample  plan  design,  standard  operating  procedures  for  safe  deployment/retrieval  of  modern  oceanographic  sampling  equipment,  accurate  recording  of  metadata  associated  with  each  sampling  station,  advanced  laboratory  sample  analysis  methods,  and  robust  data  analysis.  Direct  operation  of  the  onboard  instruments  helps  students  to  appreciate  the  limitations  of  various  sensing  technologies  and  to  critically  evaluate  the  data  they  collect.  During  the  cruise,  students  gradually  assume  greater  responsibility  for  deployment  and  data  management.  

Upon  return  to  Woods  Hole  for  the  second  shore  component,  each  research  team  completes  data  analysis  and  production  of  their  original  scientific  manuscript  and  poster.  The  manuscript  will  be  written  per  the  guidelines  of  a  selected  high-­‐impact  scientific  journal.  Students  present  their  research  findings  in  the  professional  setting  of  a  capstone  Symposium.    

This  course  consists  of  2  workshops  (10  hours  combined),  supervised  project  mentoring/work  sessions  (32  hours  combined),  a  final  Symposium  (4  hrs),  and  a  minimum  of  48  hours  of  supervised  laboratory  watch  participation  (active  learning/laboratory)  across  ~25  underway  days  at  sea.      

SEA  Semester®:  Marine  Biodiversity  &  Conservation  

www.sea.edu              Directed  Oceanographic  Research  -­‐  2  

Learning  Outcomes:  Students  will  be  able  to.  .  .  

1. demonstrate  safe  deployment/retrieval  and  describe  underlying  operating  principles  and  inherent  limitations  of  standard  oceanographic  sampling  equipment:  hydrographic  winch,  Conductivity  Temperature  and  Depth  (CTD)  profiler,  in  situ  fluorometer  to  measure  chlorophyll-­‐a  concentration,  hull-­‐mounted  Acoustic  Doppler  Current  Profiler  (ADCP)  to  measure  ocean  currents,  full  ocean  depth  profiler  for  acoustic  seafloor  mapping,  surface  and  subsurface  nets  for  zooplankton  sampling.  

2. demonstrate  accurate  data  recording  and  participate/contribute  as  an  essential  member  of  a  working  research  laboratory.  

3. critically  analyze  and  interpret  authentic  oceanographic  data.  4. generate  clear  and  accurate  visual  representations  of  oceanographic  data.  5. compose  a  professional-­‐quality  manuscript  and  deliver  a  professional  scientific  

presentation.    6. convey  scientific  research  results  to  scientific  as  well  as  lay  audiences.    

 Evaluation:    On-­‐Watch  Performance  Evaluation     15%  Laboratory  Practical  Exam   10%  Results  Updates      5%  Manuscript  Section  Revisions/Drafts      5%  Research  Press  Release      5%  Final  Manuscript   25%  Symposium  Poster  and  Poster  Presentation   20%  Peer/Self  Evaluation  of  Team  Contribution   15%    Assignments:    On-­‐Watch  Performance  Evaluation:  Much  of  the  practical  learning  will  occur  at  all  hours  of  day  and  night  as  students  and  crew  carry  out  all  scientific  operations  of  the  laboratory  watch.  The  Assistant  Scientists  are  best  able  to  evaluate  overall  progress,  including  performance  in  and  knowledge  of  lab  routines  as  well  as  the  disposition  each  student  brings  to  watch.    

Practical  Exam:  One  practical  exam  will  be  administered  to  test  understanding  of  deployment  and  analytical  methods,  lab  routines,  and  lab  safety.  

Results  Updates:  At  least  two  brief  progress  reports  will  be  expected  during  the  research  cruise.  Each  report  will  identify  successes,  challenges,  and  modifications  to  research  project,  as  well  as  include  a  list  of  sampling  stations  and  completed  morphological  identifications  and  molecular  sample  processing  to  date.  

Manuscript  Section  Revisions/Drafts:  Revisions  to  the  Methods  described  in  your  research  proposal  will  be  necessary  once  the  sampling  plan  is  implemented  at  sea.  Research  teams  will  also  submit  drafts  versions  of  Results  and  Discussion  sections  for  review.  

 

SEA  Semester®:  Marine  Biodiversity  &  Conservation  

www.sea.edu              Directed  Oceanographic  Research  -­‐  3  

Research  Press  Release:  In  an  effort  to  practice  communication  of  scientific  results  to  the  audiences  outside  the  scientific  community,  research  teams  will  compose  a  press  release  announcing  the  results  of  their  research.  The  press  release  will  be  shared  with  invited  Symposium  participants  and  used  by  SEA  to  promote  the  Symposium  event.  

Final  Manuscript:  Research  teams  will  produce  a  written  manuscript  following  guidelines  for  a  selected  high-­‐impact  scientific  journal.  There  is  an  expectation  of  professional  quality  work.  The  final  manuscripts  will  be  archived  at  SEA.  

Symposium  Poster  and  Poster  Presentation:  Research  teams  will  present  their  research  during  the  capstone  Symposium.  After  an  initial  review  and  editing  process,  posters  will  be  professionally  printed.  Emphasis  will  be  placed  on  accurate  and  clear  visual  representation  of  the  data  and  interpretation,  as  well  as  oral  explanation  of  the  work.  There  is  expectation  of  fluency  in  the  supporting  literature  to  contextualize  research  results.    

Peer/Self  Evaluation  of  Team  Contribution:  Candid  self  and  peer  evaluations  of  research  project  contributions  will  be  completed.  Emphasis  will  be  placed  on  identifying  individual  strengths  and  weaknesses  in  the  context  of  collaborative  work.      Expectations  and  Requirements:    

• Punctual  attendance  is  required  at  every  class  meeting.  • Active  participation  in  class  discussion  is  expected.  • Late  assignment  submissions  are  not  accepted.  • The  policy  on  academic  accuracy,  quoted  below,  will  be  strictly  followed  in  this  class.  

The  papers  that  you  submit  in  this  course  are  expected  to  be  your  original  work.  You  must  take  care  to  distinguish  your  own  ideas  and  knowledge  from  wording  or  substantive  information  that  you  derive  from  one  of  your  sources.  The  term  “sources”  includes  not  only  published  primary  and  secondary  material,  but  also  information  and  opinions  gained  directly  from  other  people  and  text  that  you  cut  and  paste  from  any  site  on  the  Internet.    The  responsibility  for  learning  the  proper  forms  of  citation  lies  with  you.  Quotations  must  be  placed  properly  within  quotation  marks  and  must  be  cited  fully.  In  addition,  all  paraphrased  material  must  be  acknowledged  completely.  Whenever  ideas  or  facts  are  derived  from  your  reading  and  research,  the  sources  must  be  indicated.  (Harvard  Handbook  for  Students,  305)  

• Considerations  for  use  of  internet  sources:  As  you  browse  websites,  assess  their  usefulness  very  critically.  Who  posted  the  information  and  why?  Can  you  trust  them  to  be  correct?  Authoritative?  Unbiased?  (It’s  okay  to  use  a  biased  source  as  long  as  you  incorporate  it  knowingly  and  transparently  into  your  own  work.)  Keep  track  of  good  sources  that  might  be  useful  for  subsequent  assignments,  and  annotate  in  your  bibliography  any  sites  you  cite.  Your  annotation  should  include  the  name  of  the  author  or  organization  originating  any  material  that  you  reference.  If  you  can’t  identify  the  source,  don’t  use  it!  

 Required  Reading:    Hall  BG.  2013.  Building  phylogenetic  trees  from  molecular  data  with  MEGA.  Mol.  Biol.  Evol.  30:  

1229-­‐1235.  

SEA  Semester®:  Marine  Biodiversity  &  Conservation  

www.sea.edu              Directed  Oceanographic  Research  -­‐  4  

Course  Calendar:      Topic   Readings/Assignments  Due  Week  1  (14  hrs,  at  sea)    Phase  I  Practical  Responsibilities:  

• Introduction  to  Shipboard  Laboratory  • Oceanographic  Equipment  Capabilities  • Safe  Deployment  of  Sampling  Equipment  

Research  Project  Methods  Refinement  

Results  Update  I  Due  

Week  2  (16  hrs,  at  sea)    Continued  Phase  I  Practical  Responsibilities  Project  Mentoring/Work  Sessions  

Results  Update  II  Due  Laboratory  Practical  Exam  

Week  3  (6  hrs,  Bermuda  port  stop)    Project  Mentoring/Work  Sessions   Methods  Revision  Due  

Week  4  (16  hrs,  at  sea)    Phase  II  Practical  Responsibilities:  

• Master  Lab  Routines  and  Sampling  Methods  • Apprentice  Lab  Manager  

Project  Mentoring/Work  Sessions  

 

Week  5  (16  hrs,  at  sea)    Continued  Phase  II  Practical  Responsibilities  Project  Mentoring/Work  Sessions  

Morphological  Results  Due  

Week  6  (20  hrs,  SEA  campus)    Bioinformatics  Workshop  Data  Analysis  Work  Sessions  Manuscript  Writing  Sessions  

Hall  2013  Research  Press  Release  Due  Draft  Results/Discussion  Due  

Week  7  (2  hrs,  SEA  campus)    Communications  Workshop:  Poster  Presentation   Final  Manuscript  Due  

Draft  Poster  Due  

Week  8  (4  hrs,  SEA  campus)    Symposium   Final  Poster  Due  

Peer/Self  Evaluation  Due