NOAA Ship: NOAA Ship David Starr Jordan

Cruise Number: DS-09-01
Cruise Dates: March 7 - 24, 2009
Cruise Title: CalCOFI Survey.
Study Area: US/Mexican border to Avila Beach, CA out to 400 nautical miles.


  • Ship loading and gear preparation: 02 - 05 MAR.
  • Leg 1: 07 MAR - Station 93.3/26.7; 24 MAR - Arrive San Francisco, CA
  • The ship will offload scientific gear in San Francisco, CA.

Tracklines and station positions are included at the end of this document in Appendix1.
Sponsoring Institution: NOAA/NMFS, Southwest Fisheries Science Center (SWFSC) , Fisheries Resources Division (FRD)

Cruise Description and Objectives:

  1. To conduct continuous underway sampling of surface waters.  Temperature and salinitywill be automatically logged by computer with the output from the GPS navigational unit.
  2. To record current profiles throughout the duration of the cruise with the Acoustic Doppler Current Profiler.
  3. To continue an ongoing assessment of pelagic fish stocks between La Jolla and Avila Beach, California.
  4. To monitor environmental conditions within the CalCOFI survey area.
  5. To make continuous observations of sea birds and marine mammals.
  6. To record continuous acoustic targets obtained with the EK-500 or EK-60 scientific sounder.

Chief Scientist: David A. Griffith, SWFSC (858) 546-7155,  This email address is being protected from spambots. You need JavaScript enabled to view it.


1.1 - The Jordan will conduct operations in the Southern California Bight as well as occupying line 76.7 just north of Point Conception.
 1.1.1 - Each standard CalCOFI station will include the following:  CTD/Rosette - consisting of 24 10-liter hydrographic bottles will be lowered to 500 meters (depth permitting) to measure physical parameters and collect water at discrete depths for analysis of: salinity, nutrients and chlorophyll.  CalBOBL (CalCOFI Bongo) - standard oblique plankton tow with 300 meters of wire out, depth permitting, using paired 505 µm mesh nets with 71 cm diameter openings.  The technical requirements for this tow are: Descent wire rate of 50 meters per minute and an ascent wire rate of 20 meters per minute.  All tows with ascending wire angles lower than 38° or higher than 51° in the final 100 meters of wire will be repeated.  Additionally, a 45° wire angle should be closely maintained during the ascent and descent of the net frame.  Manta net (neuston) tow - using a 505 µm mesh net on a frame with a mouth area of 0.1333 m².  Tows are 15 minutes in duration at towing speed of approximately 1.5 - 2.0 knots.  Wire angles should be kept between 15° and 25°.  Weather observations.  Pairovet net - will be fished from 70 meters to the surface (depth permitting) using paired 25 cm diameter 150 µm mesh nets out to and including station 70. The technical requirements for Pairovet tows are: Descent rate of 70 meters per minute, a terminal depth time of 10 seconds and an ascent rate of 70 meters per minute.  All tows with wire angles exceeding 15° during the ascent will be repeated.  PRPOOS (Planktonic Rate Processes in Oligotrophic Ocean Systems) net ­will be taken at all stations on line 90.0 and 80.0 as well as stations out to and including station 70.0 on lines 86.7 and 83.3. These stations are occupied as part of the LTER (Long Term Ecological Research) project.  The mesh of the PRPOOS net is 202 µm and the tow is a vertical cast up from 210 meters.  Primary productivity - at about 1100 hours on each day of the cruise a primary productivity CTD cast consisting of six 10-liter hydrographic bottles will be carried out. The cast arrangement will be determined by a Secchi disc observation. The purpose of the cast is to collect water from six discrete depths for daily in situ productivity experiments.  Measurements of extracted chlorophyll and phaeophytin will be obtained with a fluorometer.  Primary production will be measured as C14 uptake in a six hour in situ incubation. Nutrients will be measured with an auto-analyzer.  All radioisotope work areas will be given a wipe test before the departure of the SIO technical staff.  Light meter - will be used to measure the light intensity in the euphotic zone once a day with the primary productivity cast.
1.1.2  Thermosalinometer Sampling - The ship will provide and maintain a thermosalinometer (TSG), which is calibrated and in working order, for continuous measurement of surface water temperature and salinity.  A backup unit (calibrated and in working order) will also be provided by the vessel and remain aboard during the cruise. The Scientific Computing System (SCS) will serve as the main data collection system..  All SCS data will be provided to SWFSC personnel at the completion of the cruise.
1.1.3  Acoustics –The scientific EK-60 (or EK-500) depth sounder will be operated, at 38, 120 and 200 KHz and interfaced to a data acquisition system to estimate micronekton biomass between 0 and 500 m. The vessel's EQ-50 depth sounder may be used at the discretion of the Commanding Officer, but will normally remain off while underway. The ship shall inform the Cruise Leader of any use of the vessel's EQ-50, as it interferes with the signals received on the scientific EK-60. Its use will be continuous.
1.1.4  Marine mammal and sea bird observations - During transit between stations, a bird observer and marine mammal observer will be recording location and species of various birds and marine mammals.
1.1.5  Acoustic hydrophone - During transit between most daylight stations, an acoustic hydrophone array will be towed from the stern with the net reel to record sounds from marine mammals.  Upon approaching a station, a sonobuoy will be deployed one nautical mile prior to stopping for station work.
1.1.6  CUFES - The egg pump will be mounted inside the ship’s hull drawing water from a depth of three meters.  During the grid occupation, the pump will run continuously between stations to sample any pelagic fish eggs.
1.1.7  SCCOOS - An additional nine stations will be occupied within the CalCOFI pattern for SCCOOS (S. California Coastal Ocean Observation System).  These are 20 meter depth stations and will consist of a CTD lowered to within a few meters from the bottom and a Bongo tow. These stations are included in the original station plans provided to the ship.

2.1 Chief Scientist - The Chief Scientist is David A. Griffith, SWFSC, at phone (858) 546-7155.
The Chief Scientist is authorized to alter the scientific portion of this cruise plan with the concurrence of the Commanding Officer, provided that the proposed changes will not:
(1) jeopardize the safety of personnel or the ship, (2) exceed the time allotted for the cruise, (3) result in undue additional expense, or (4) change the general intent of the project.
2.2 Participating Scientists
Please see Appendix 3.
2.3 Medical Forms - All scientific personnel will complete a NOAA Health Services Questionnaire (NHSQ) prior to embarking, as per NC Instruction 6000.  This form will be routed through MOP Health Services for approval 30 days prior to the cruise.

3.1 Supplied by scientific party:
  1. -80°C Freezer (SWFSC)
  2. 37% Formalin (SWFSC)
  3. Ethanol (SWFSC)
  4. Tris buffer (SWFSC)
  5. Sodium borate (SWFSC)
  6. 30 cc and 50 cc syringes (SWFSC)
  7. Canulas (SWFSC)
  8. Pint, quart and gallon jars (SWFSC)
  9. Inside and outside labels (SWFSC)
  10. CalCOFI net tow data sheets (SWFSC)
  11. 71 cm CalCOFI Bongo frames (SWFSC)
  12. 71 cm CalCOFI 505 µm mesh nets (SWFSC)
  13. CalCOFI 150 µm Calvet nets and codends (SWFSC)
  14. CalCOFI Pairovet frames (SWFSC)
  15. 333 µm mesh codends (SWFSC)
  16. Inclinometer for bongo tows (SWFSC)
  17. Digital flowmeters (SWFSC)
  18. PRPOOS frames (SIO)
  19. 170 lb PRPOOS weight (SIO)
  20. 202 µm mesh PRPOOS nets and codends (SIO)
  21. 75 lb Bongo weight (SWFSC)
  22. 100 lb hydro weights (SWFSC)
  23. CalCOFI Manta net frames (SWFSC)
  24. 60 cm CalCOFI 505 µm mesh Manta nets (SWFSC)
  25. Standard CalCOFI tool boxes (SWFSC)
  26. Bucket thermometers and holders (SWFSC)
  27. Hand held inclinometer for Pairovet tows(SWFSC)
  28. Oxygen auto-titration rig with reagents (SIO)
  29. Oxygen flasks (SIO)
  30. Guildeline Portasal (SWFSC, SIO)
  31. Salinity bottles (SIO)
  32. Standard sea water (SIO)
  33. Data sheets for scheduled hydrographic work (SIO)
  34. Weather observation sheets (SIO)
  35. Primary productivity incubation rack (SIO)
  36. C14 and other chemicals for primary productivity work (SIO)
  37. CTD and rosette (SIO)
  38. 10 liter hydrographic bottles (SIO)
  39. Turner fluorometer (SIO)
  40. 90% acetone and all supplies for chlorophyll extraction (SIO)
  41. Nutrient vials (SIO)
  42. Isotope van (SIO)
  43. LTER van (SIO)
  45. Marine mammal hydrophone (SIO)
  46. Disposable sonobuoys (SIO)

3.2 Supplied by ship - We request the following systems and their associated support services, sufficient consumables, back-up units, and on-site spares.  All measurement instruments are assumed to have current calibrations and we request that all pertinent calibration information be included in the data package.

  1. Starboard hydro winch with ¼” cable for standard Bongo, Pairovet and Manta tows
  2. Port winch with .322" conductive cable
  3. J-frame w/block to accommodate .322" cable
  4. Net reel for acoustic array deployment
  5. Constant temperature room set at 22°C ±1°C (71.5°F ±2°F)
  6. Winch monitoring system
  7. Seabird thermosalinometer
  8. Knudsen 12 kHz depth recorder
  9. Acoustic Doppler Current Profiler w/writeable CD drive

3.3 Installation and Maintenance - Prior to departure from San Diego the Chief Scientist and members of the scientific party may board the vessel, with permission of the Commanding Officer, to test survey equipment and environmental sensors.  It is also requested that the constant temperature room be set at 22°C ±1°C (71.5°F ±2°F) prior to departure.

3.4 Hazardous Materials  - The Chief Scientist shall be responsible for complying with NC Instruction 6280a, Hazardous Materials and Hazardous Waste; policy, guidance, and training, dated February 4, 1991, paragraph 7.g and paragraph 9. By Federal Law, the ship may not sail without a complete inventory of Material Safety Data Sheets (MSDS's) and appropriating neutralizing agents, buffers, and/or absorbents in amounts adequate to address spills of a size equal to the amount of chemicals brought on board.  The Chief Scientist will provide the Commanding Officer with a copy of all MSDS's prior to the cruise.


4.1 Collection of Data - The Chief Scientist will receive all original data related to the project. The Chief Scientist will in turn furnish the Commanding Officer with a complete inventory listing of all data gathered by the scientific party, detailing types of operations and quantities of data prior to departing the ship.  All data gathered by the vessel's personnel that are desired by the Chief Scientist will be released to the Chief Scientist, including supplementary data specimens and photos gathered by the scientific crew.

4.2 Dissemination of Data - The Chief Scientist is responsible for the quality assurance, disposition and archiving of data and specimens collected aboard the ship.  The Chief Scientist is also responsible for the dissemination of copies of these data to cruise participants and to any other requesters. The SWFSC cruise report will be submitted according to SWFSC procedures to appropriate persons and groups.

4.3 Evaluation Form - The Chief Scientist will complete the Ship Operations Evaluation Form and forward it to the Office of Marine and Aviation Operations.  The Commanding Officer will provide this form.


5.1 Ancillary Projects - Ancillary projects are secondary to the objectives of the cruise,
should be treated as additional investigations, do not have representation aboard, and are accomplished by the ship's force.  Ancillary tasks will be accomplished in accordance with the NOAA Fleet Standing Ancillary Instructions. Any additional work will be conducted so as not to interfere with operations as outlined in these instructions. The Chief Scientist will be responsible for determining the priority of additional work relative to the primary project with approval from the Commanding Officer.


6.1 Radios - The Cruise Leader or designee may request, from the Commanding Officer, the use of radio transceivers aboard the ship to communicate with other vessels and aircraft, if necessary.

6.2 Telephone - The Cruise Leader or designee may require access to the ship's INMARSAT or cellular telephone systems with permission from the Commanding Officer.  The Commanding Officer will provide the Cruise Leader with a log of all INMARSAT calls made from the ship for SWFSC business at the end of each leg.  In accordance with the Communications Reimbursement Policy, SWFSC will pay these charges via a transfer of funds from SWFSC to the ship.

6.3 Electronic Mail - All members of the scientific party will have access to e-mail for communications with persons not aboard the ship.  The amount of such communication traffic will be determined by the Chief Scientist.

6.4 Routine Reports - The Cruise Leader will submit a weekly cruise report, along with time and attendance for the scientific party, to the Survey Coordinator each Thursday during the cruise via e-mail or, if e-mail is not functioning properly, via fax.


7.1 Pre-cruise Meeting - A pre-cruise meeting between the Chief Scientist and the Commanding Officer (and his staff) will be held prior to the start of the cruise to identify operational requirements (i.e., overtime, modifications, repairs or procurement).  The date and time for this meeting is yet to be scheduled.

7.2 Underway Meetings - Meetings between the Commanding Officer (and other officers) and the Cruise Leader should occur at the beginning and end of each leg to discuss and solve any problems or changes that may arise.  Additional meetings should occur as needed.

7.3 Debrief - A post-cruise debriefing will be held between the Chief Scientist and the Commanding Officer.  If serious problems are identified, the Commanding Officer shall notify the Marine Operations Center, Pacific, in the most direct means available.  The Chief Scientist shall document identified problems in the Ship Operations Evaluation Form.  The time and date for the debrief will be determined toward the end of the cruise.

7.4 Time and Attendance - Time and Attendance will be filled out by the SWFSC timekeeper while the ship is at sea, based on information transmitted by the Cruise Leader to the Survey Coordinator. Scheduled overtime is authorized for Saturdays, Sundays, holidays and any hours over a standard eight hour week day. Irregular overtime will be authorized by the Cruise Leader as required. SWFSC personnel are authorized per diem at the rate of $3.00 per day to be paid via a travel voucher at the termination of the cruise. Task Number 28LEF01-P15 will pay for per diem and overtime for any SWFSC permanent, term or temporary employees. 

7.5 Navigation - Primary control will be GPS, also dead reckoning based on visual bearings and radar ranges when possible.

7.6 Scientific Spaces - The Cruise Leader shall be responsible for the proper upkeep and cleaning of all spaces assigned to the scientific party, both laboratory and living spaces, throughout the cruise. The Cruise Leader or Chief Scientist will make berthing assignments for scientific personnel on a per-leg basis, with approval of the Commanding Officer.

7.7 Foreign Nationals Access to NMAO Vessels ­Please see Appendix 4.
For further information contact Sam McClatchie, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8604 La Jolla Shores Drive, La Jolla, CA 92037; This email address is being protected from spambots. You need JavaScript enabled to view it., Phone (858) 546-7083.  More information about the cruise and project can be found at the project’s website:
Appendix 1. NOAA Ship David Starr Jordan track lines for CalCOFI 0903JD

Appendix 2. Station positions:

Line  Station Dlatitude  Dlongitude 
01  93.3  26.7  32.95637243  117.3053809 
02  93.4  26.4  32.94905192  117.2735654 
03  91.7  26.4  33.24350056  117.4654169 
04  93.3  28  32.91303909  117.3943818 
05  93.3  30  32.84637243  117.5312206 
06  93.3  35  32.67970576  117.8728643 
07  93.3  40  32.51303909  118.2138649 
08  93.3  45  32.34637243  118.5542278 
09  93.3  50  32.17970576  118.8939582 
10  93.3  55  32.01303909  119.2330612 
11  93.3  60  31.84637243  119.5715421 
12  93.3  70  31.51303909  120.2466579 
13  93.3  80  31.17970576  120.9193461 
14  93.3  90  30.84637243  121.5896467 
15  93.3  100  30.51303909  122.2575992 
16  93.3  110  30.17970576  122.9232422 
17  93.3  120  29.84637243  123.5866142 
18  90.0  120  30.41794919  123.9989326 
19  90.0  110  30.75128253  123.3316429 
20  90.0  100  31.08461586  122.6620162 
21  90.0  90  31.41794919  121.9900131 
22  90.0  80  31.75128253  121.3155939 
23  90.0  70  32.08461586  120.6387183 
24  90.0  60  32.41794919  119.9593451 
25  90.0  53  32.65128253  119.4822756 
26  90.0  45  32.91794919  118.9355113 
27  90.0  37  33.18461586  118.3870812 
28  90.0  35  33.25128253  118.2497109 
29  90.0  30  33.41794919  117.9058212 
30  90.0  28  33.48461586  117.7680788 
31  90.0  27.7  33.49461586  117.7474083 
32  88.5  30.1  33.67442348  118.0836933 
33  86.8  32.5  33.88887212  118.4442347 
34  86.7  33  33.88952596  118.4903339 
35  86.7  35  33.82285929  118.6287319 
36  85.4  35.8  34.02135923  118.8341306 
37  86.7  40  33.65619263  118.9742516 
38  86.7  45  33.48952596  119.3190964 
39  86.7  50  33.32285929  119.6632718 
40  86.7  55  33.15619263  120.0067835 
41  86.7  60  32.98952596  120.3496367 
42  86.7  70  32.65619263  121.0333897 
43  86.7  80  32.32285929  121.7145734 
44  86.7  90  31.98952596  122.3932299 
45  86.7  100  31.65619263  123.0694006 
46  86.7  110  31.32285929  123.7431265 
47  83.3  110  31.91175657  124.1703953 
48  83.3  100  32.2450899  123.4923224 
49  83.3  90  32.57842323  122.8117321 
50  83.3  80  32.91175657  122.1285823 
51  83.3  70  33.2450899  121.4428307 
52  83.3  60  33.57842323  120.7544339 
53  83.3  55  33.7450899  120.4092298 
54  83.3  51  33.87842323  120.1325788 
55  83.3  42  34.17842323  119.5085132 
56  83.3  40.6  34.2250899  119.4112355 
57  83.3  39.4  34.2650899  119.3278113 
58  81.7  43.5  34.40555136  119.80037 
59  81.8  46.9  34.27489752  120.0252367 
60  80.0  50.5  34.46666667  120.4890554 
61  80.0  51  34.45  120.5239048 
62  80.0  55  34.31666667  120.802448 
63  80.0  60  34.15  121.15 
64  80.0  70  33.81666667  121.8430351 
65  80.0  80  33.48333333  122.5333494 
66  80.0  90  33.15  123.2209872 
67  80.0  100  32.81666667  123.9059922 
68  76.7  100  33.38824343  124.3228913 
69  76.7  90  33.72157677  123.633345 
70  76.7  80  34.0549101  122.9410906 
71  76.7  70  34.38824343  122.2460832 
72  76.7  60  34.72157677  121.5482772 
73  76.7  55  34.88824343  121.1983102 
74  76.7  51  35.02157677  120.9178206 
75  76.7  49  35.08824343  120.7774028 
Arrive San Francisco 

Appendix 3. Personnel for the CalCOFI 0903JD survey 
David Starr Jordan  Leg I: 
Position  Name  Affiliation  Berth 
Chief Scientist  Dave Griffith  SWFSC 
Fishery Biologist  Dimitry Abramenkoff  SWFSC 
Fishery Biologist  Amy Hays  SWFSC 
Biologist Bryan Overcash CDFG
Oceanographer Jim Wilkinson  SIO
Oceanographer Grant Susner  SIO
Oceanographer Jennifer Sheldon SIO
Oceanographer Dave Faber SIO
Oceanographer Shonna Dovel SIO
Oceanographer Megan Roadman SIO
Chemist Dan Schuller SIO
Marine Mammal Biologist Greg Campbell SIO
Marine Mammal Biologist Andrea Havron SIO

Appendix 4. Foreign National Access
Foreign National Access and Deemed Export Controls on NMAO Vessels
All foreign national access to the vessel shall be in accordance with NAO 207-12 and RADM De Bow’s March 16, 2006 memo (  The foreign national’s sponsor is responsible for obtaining clearances and export licenses required and for providing for required escorts by the NAO. Programs sponsoring foreign nationals should consult with their designated line office personnel to assist with the process (
The following are basic requirements.  Full compliance with NAO 207-12 is required.
Responsibilities of the Chief Scientist:
Ensure the following is provided to the Commanding Officer before any foreign national will be allowed on board for any reason:
1.  Written notification identifying the NOAA Program individual who is responsible for ensuring compliance with NOAA and export regulations for the foreign national (see Foreign National Sponsor responsibilities below).
2.  A copy of the DOC/OSY clearance authorization for access by the foreign national.
3.  A copy of Appendix B of NAO 207-12 with NOAA Chief Administrative Officer concurrence endorsement.
4.  Written notification that the foreign national has been cleared against the State, Commerce and Treasury departments' Lists to Check.
5.  Provide the NOAA Foreign National List spreadsheet for each foreign national in the scientific party.

Escorts – The Chief Scientist is responsible to provide escorts to comply with NAO 207-12 Section 5.10, or as required by the vessel’s DOC/OSY Regional Security Officer.
Ensure all non-foreign national members of the scientific party receive the briefing on Espionage Indicators (NAO 207-12 Appendix A) at least annually or as required by the servicing Regional Security Officer.
Export Control - The Chief Scientist is responsible for complying with NAO 207-12 and the development of Technology Access Control Plans for items they bring aboard.  The Chief Scientist must notify the Commanding Officer of any export controlled items they bring aboard and any access restrictions associated with these items. 
The Commanding Officer and the Chief Scientist will work together to implement any access controls necessary to ensure no unlicensed export occurs of any controlled technology onboard regardless of ownership.
Responsibilities of the Commanding Officer:
Ensure only those foreign nationals with DOC/OSY clearance are granted access..
Deny access to OMAO platforms and facilities by foreign nationals from countries controlled for anti-terrorism (AT) reasons and individuals from Cuba or Iran without written NMAO approval and compliance with export and sanction regulations.
Ensure foreign national access is permitted only if unlicensed deemed export is not likely to occur.
Ensure receipt from the Chief Scientist of the NOAA Foreign National List spreadsheet for each foreign national in the scientific party.
Ensure Foreign Port Officials, e.g., Pilots, immigration officials, receive escorted access in accordance with maritime custom to facilitate the vessel’s visit to foreign ports.
Export Control - 8 weeks in advance of the cruise, provide the Chief Scientist with a current inventory of OMAO controlled technology onboard the vessel and a copy of the vessel Technology Access Control Plan (TACP). Also notify the Chief Scientist of any OMAO-sponsored foreign nationals that will be onboard while program equipment is aboard so that the Chief Scientist can take steps to prevent unlicensed export of Program controlled technology.
The Commanding Officer and the Chief Scientist will work together to implement any access controls necessary to ensure no unlicensed export occurs of any controlled technology onboard regardless of ownership.
Ensure all OMAO personnel onboard receive the briefing on Espionage Indicators (NAO 207-12 Appendix A) at least annually or as required by the servicing Regional Security Officer.
Responsibilities of the Foreign National Sponsor
Export Control - The foreign national’s sponsor is responsible for obtaining any required export licenses and complying with any conditions of those licenses prior to the foreign national being provided access to the controlled technology onboard regardless of the technology’s ownership.
The Departmental Sponsor/NOAA of the foreign national shall assign an on-board Program individual, who will be responsible for the foreign national while on board. The identified individual must be a U.S. citizen, NOAA employee or be approved by the vessel’s DOC Regional Security Officer homeport. 
Ensure completion and submission of Appendix C (Certification of Conditions and Responsibilities for a Foreign National Guest) as required by NAO 207-12 Section 5.03.h