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Miller Freeman Cruise MF-01-01, Leg 1

January 28-February 5, 2001


Morgan Busby, Chief Scientist
NOAA Alaska Fisheries Science Center
7600 Sand Point Way, NE
Seattle, Washington 98115


RADM Nicholas Prahl, Director Pacific Marine Center
Seattle, WA 98102

/s/ Eddie N. Bernard
Dr. Eddie N. Bernard, Director
Pacific Marine Environmental Laboratory
Seattle, WA 98115
/s/ James M. Coe
Dr. James M. Coe, Science and Research Director
Alaska Fisheries Science Center
Seattle, WA 98115





Cruise No: MF01-01, Leg 1
FOCI No: 1MF01
December 20, 2000


These instructions, with FOCI Standard Operating Instructions for NOAA Ship MILLER
FREEMAN dated December 11, 2000 present complete information for this cruise.


Northern Gulf of Alaska


Depart Kodiak, AK 1200 January 28, 2001 TNG
Arrive Dutch Harbor, AK 1200 February 5, 2001 TNG

Participating organizations:

NOAA - Alaska Fisheries Science Center (AFSC)
NOAA - Pacific Marine Environmental Laboratory (PMEL)


Fisheries-Oceanography Coordinated Investigations (FOCI) is an effort by NOAA and associated academic scientists. At present, FOCI consists of a Shelikof Strait (western Gulf of Alaska) walleye pollock project, and a NOAA Coastal Ocean Program project: Southeast Bering Sea Carrying Capacity. FOCI also supports associated projects, such as the Arctic Research Initiative, and U.S. GLOBEC, that address scientific issues related to FOCI. FOCI's goal is to understand the effects of abiotic and biotic variability on ecosystems of the North Pacific Ocean and Bering Sea in order to discern the physical and biological processes that determine recruitment variability of commercially valuable finfish and shellfish stocks in Alaskan waters.


We will be conducting bottom trawl sampling on the outer continental shelf and upper slope in the Gulf of Alaska beginning near Kodiak Island and ending near Sanak Island to collect ripe adult arrowtooth flounder (ATF). We will also be deploying deep bongo plankton tows to collect their eggs. This work is needed to establish the appearance of arrowtooth flounder eggs in the plankton, so they can be identified with confidence in samples. Data on physical characteristics of water in the area will also be collected.


1.1. Chief Scientist:
Busby, Morgan     M/USA
(206) 526-4113

The Chief Scientist has the authority to revise or alter the technical portion of the instructions as work progresses provided that, after consultation with the Commanding Officer, it is ascertained that the proposed changes will not: (1) jeopardize the safety of personnel or the ship; (2) exceed the overall time allotted for the project; (3) result in undue additional expenses; (4) alter the general intent of these project instructions.

1.2 Participating Scientists:
Blood, Deborah F USA NOAA/AFSC
Chilton, Elizabeth F USA NOAA/AFSC
Floering, William M USA NOAA/PMEL
Matarese, Ann F USA NOAA/AFSC
Muto, Fumihito M JAPAN HokkaidoUniversity

1.3 NOAA Pacific Marine Center Operations Contact:

Larry Mordock
NOAA/Marine Operations Center-Pacific (MOP/1)
1801 Fairview Ave. East
Seattle, WA 98102-3767
(206) 553 - 4764

1.4 Program Contacts:

Dr. Jeffrey Napp
7600 Sand Point Way NE
Seattle, WA 98115
(206) 526-4148


A standard oceanographic watch will be utilized which consists of a winch operator, a scientific staff of two and a Survey Tech on deck. Operations will be conducted 24 hours a day. A fishing crew will be required to assist with bottom trawls which will be conducted in daytime and nighttime.


Ship will proceed to the vicinity of line A, station 1 (appendices 1 and 2), and locate trawlable bottom at a depth of 200 m to deploy the first bongo tow and bottom trawl. This sampling will be repeated at two stations along a line moving offshore at depths of 400 and 600 m. Five additional lines (B-F) consisting of three stations of 200, 400, and 600 m depth are planned to be occupied during the survey.  Whenever ATF eggs or ripe adults are found, a CTD cast with bottles will be deployed to collect data on the physical properties of water at the bottom and water for holding live eggs. We will then attempt to fertilize eggs from gravid females with sperm from ripe males aboard ship. Live eggs will be held in gallon jars placed in a constant temperature referigerator at 3-4ø C until the end of the cruise. If ripe female and male ATF are not collected, a sample of up to 50 adult ATF will be lengthed and dissected to determine sex and estimate maturity state. Bottom trawl and bongo sampling will continue until time allotted for the survey expires regardless of whether or not ripe adult ATF or suspected ATF eggs are found. A representative of the RACE Division, Alaska Fisheries Science Center, in Seattle, WA will contact the Miller Freeman by Inmarsat if ripe adult ATF are encountered in the Alaska commercial fishery and reported by the Observer Program. In this event, operations will be moved to the locality reported, if within the time constraints of the cruise.


The following are operations to be conducted on this cruise. The procedures for these operations are listed in the FOCI SOI. Operations not addressed in the SOI and changes to standard procedures are addressed below.

Bottom trawl
MARMAP bongo tow (SOI 2.2.2)
CTD/Water samples (SOI 2.2.1)
EK500 monitoring (SOI 2.2.12)

A poly nor'eastern bottom trawl with roller gear will be used to collect live adult ATF to spawn on board ship to obtain live fertilized eggs. After deployment and settling of the net on bottom, it will be towed for 15 minutes at a speed of 1.5 m/sec. Location and duration of trawls, however, may be altered if bottom conditions will not allow a complete haul. ATF will be the only species processed from the catch. In the event of a large catch, only subsamples of ATF will be processed. Eggs will be stripped from gravid ATF females and mixed with milt from ripe males and then counted and placed in gallon jars and held in a constant temperature refrigerator at 3-4ø C until the end of the cruise. Niskin bottles (10 liter) will be deployed to collect water at the bottom for holding and transporting eggs. Bongo tows using the 60 cm array will be conducted at each station. Bongo tows will be deployed to within 10 m of the bottom to a maximum depth of 500 m. From each bongo tow, one sample will be examined at sea for the presence of possible ATF eggs and the other will be preserved and processed ashore. At the end of the cruise, any live eggs collected will placed in thermoses and coolers for transport by air to Seattle.


The following systems and their associated support services are essential to the cruise. Sufficient consumables, back-up units, and on-site spares and technical support must be in place to assure that operational interruptions are minimal. All measurement instruments are expected to have current calibrations, and all pertinent calibration information shall be included in the data package.

3.1 Equipment and Capabilities to be Provided by the Ship:

Oceanographic winch with slip rings and 3-conductor cable terminated for CTD,

Wire-angle indicator and readout for oceanographic winch,

Oceanographic winch for bongo net (and other nets when used) with slip rings and 3-conductor cable terminated for the SeaCat,

Sea-Bird 911 plus CTD system with stand (back up system) (Each CTD system should include underwater CTD, weights, and pinger and there should be one deck unit and tape recorder for the two systems),

For CTD field corrections: AUTOSAL salinometer,

Sea-Bird SBE-19 Seacat system (backup system),

Meter block for plankton tows,

Wire speed indicators and readout for quarterdeck,

Refrigerator for live fish eggs,

Blast freezer for fish specimens,

Simrad EQ-50 echo sounder ,

JRC JFV-200R color sounder recorder,

Use of Pentium PC in DataPlot for data analysis,

SCS (Shipboard Computer System),

Furuno net sounder,

Stern platform removed for trawl ramp use, Laboratory space with exhaust hood, sink, lab tables and storage space,

Sea-water hoses and nozzles to wash nets (quarterdeck and aft deck),

Sorting table,

Adequate deck lighting for night-time operations,

Navigational equipment including GPS and radar ,

Safety harnesses for working on quarter deck and fantail,

3.2 Equipment to be Provided by the Project:

Sea-Bird 911 plus CTD system

Sea-Bird SBE-19 Seacat system (primary system),

PMEL PC with SEASOFT software for CTD data collection and processing,

Fluorometer, light meter, and chlorophyll absorbance meter (ChlAM) to be mounted on CTD,

CTD stand modified for attachment of fluorometer,

Conductivity and temperature sensor package to provide dual sensors on the primary CTD,

CTD rosette sampler,

IAPSO water,

60-cm bongo sampling arrays,

Poly Nor'eastern bottom trawl with roller gear with doors,

Spare wire angle indicator,

Miscellaneous scientific sampling and processing equipment ,

Sorting tables and baskets for processing trawl catches,

Motion compensating scale,

Discrete Sample Data Base software and forms,

Microscope for examining, sorting, and measuring fish eggs,

Thermoses and coolers for transporting live eggs.

3.3. Ship's Computer System (SCS)

The ship's Scientific Computer System (SCS) shall operate throughout the cruise, acquiring and logging data from navigation, meteorological, oceanographic, and fisheries sensors. See FOCI Standard Operating Instructions for specific requirements.


Data disposition, responsibilities and data requirements are listed in the FOCI Standard Operating Instructions.


5.3 Piggyback projects:

At the beginning of the cruise, an oceanographic mooring located in Chiniak Bay will be retreived and necessary instruments serviced or replaced, and then redeployed for the Kodiak NMFS Laboratory. When time allows, fin clips and or/tissue samples will be collected from sculpins (family Cottidae) and frozen or preserved in preserved in 95% ethanol for a study of the molecular phylogeny of this family of fishes. Carcasses of the sampled fish will be labeled and frozen or preserved in 10% formalin. This sampling is being conducted for Dr. Fumihito Muto, Laboratory of Marine Biodiversity, Hokkaido University, Hakodate, Japan. In addition, we will be collecting data from Pacific ocean perch (Sebastes alutus), dusky rockfish (S. ciliatus) and northern rockfish (S. polyspinus) for an age at maturity study in the Gulf of Alaska. Fish will be selected from each haul using stratified random sampling based on two individuals per 1 cm length interval for each sex of each species. Fork length, somatic weight, gonad weight and macro-maturity stage will be recorded for each fish. Otoliths and gonads will be collected from these fish. The gonad samples will be preserved in 10% neutral buffered formalin. Digital photos of gonads may be taken of certain maturity stages for future comparison with microscopically determined maturity stages of the gonads. This sampling is being conducted for Ms. Elizabeth Chilton, Alaska Fisheries Science Center, Kodiak Laboratory.


6.5. Hazardous Materials:

The Chief Scientist shall be responsible for complying with NC Instruction 6280A, 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 MSDS, and appropriate neutralizing agents, buffers, and/or absorbents in amounts adequate to address spills of a size equal to the amount aboard.

The following hazardous materials will be provided and controlled by the scientists with the Chief Scientist assuming responsibility for the safe handling of such substances:

Ethyl Alcohol (Ethanol)


Stockards solution


7.4 Important phone numbers, fax numbers and e-mail addresses:

AFSC/RACE Fax: (206) 526-6723

MILLER FREEMAN COMSAT (government account numbers): These are much cheaper than Inmarsat
direct numbers and should always be used first.

800-678-0872, after voice prompt dial 330-394-113, after tone dial customer ID# (Voice)
800-678-0872, after voice prompt dial 761-267-348, after tone dial customer ID# (Fax)

Inmarsat (direct numbers)
011-872-330-394-113 (voice)
011-872-761-267-348 (fax)

CELLULAR: 206-660-7167
KODIAK ROAMER: 907-528-7626
(First dial the roamer, wait for dial tone, then dial cellular number.)

AFSC person:
PMC radio room:
Direct to ship:
(include the person's name in the subject field)


Appendix 1 - Approximate beginning positions for sampling lines.

Appendix 2 - Map showing line starting points (click image to view full size).

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