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Fishing for Data

August 05
The end of the beginning

​"You can have data without information, but you cannot have information without data." Daniel Keys Moran.DSC_0113.JPGSimilar to how landed fish go on to feed society and the economy, the story of the data collected on the Johan Hjort during the IBTS cruise doesn't end at the port. In fact, in many ways it is just the beginning.

The scientists on board have done their bit: the trawl net has been systematically deployed and catches sorted; various species have had samples, lengths, weights and ages taken; valuable data has been stored. All carried out with efficiency and admirable character, especially given the nature of their shift work.

It's now time for the next stage of the data's life-cycle as it is processed and cleaned to remove any inaccurate or duplicate records, before being submitted to ICES DATRAS database by IMR in September along with that from the other countries in the survey. DATRAS is a hub of facts and figures from all the trawl surveys hosted by ICES, containing fish sampling data (fisheries independent data: that gathered outside the realm of commercial fisheries) in a standardized format. It includes North Sea IBTS data harking back to 1965.

This DATRAS data can be downloaded from the ICES website as various products by ICES scientists, stock assessors, working groups, and just about anyone else (the data is open access after all) for use in research and stock assessments. Some of the downloadables include the catch per unit of effort (CPUE). In the case of IBTS, that's adjusted in DATRAS to indicate catch of fish of the same species per hour of trawling; these help produce indices of relative abundance. Also available are age-length keys, used to estimate the age structure of a fish population by extrapolating the known data taken at sea.​ ​Then there's the CTD data. ​

species sample data.JPGData stored on board the Johan Hjort, arranged by species, weight and count amongst other parametres


But this only tells part of the story. To explain the next chapter, Fishing for Data will be back in September with a post describing how some of the data collected on the North Sea during the cruise is stored, downloaded and transformed into the building blocks that go on to build the stock assessments which underpin ICES advice.​ This then goes on to guide the fishing, completing the cycle.


.....to be continued....

July 31
Cleaning down and moving on

​And so it is that after almost 12 days on board the Johan Hjort - and a full month for a couple of the scientists - we finally docked in Stavanger, ​Norway’s third largest city, scene of a 19th century herring boom and modern-day oil capital. ​

Despite how interesting and enjoyable the cruise had been, I was relieved to swap my sea legs back for the land ones I had taken off over a week ago. 

As well as cleaning down the scientific labs and packing away equipment, the ship needed to be prepared for the next and final leg of the IBTS cruise, which will embark on a hydrgraphical data-collecting mission for the next week.

The data, meanwhile, will be cleaned before being submitted to ICES DATRAS database​ sometime in September for future use by the working groups.

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The scientists and IT personnel involved in the IBTS Q3 cruise.

July 25
Birthday on board
The fish aren't the only ones whose years are being counted on board the Johan Hjort during this survey. 

Today was a special day for one of the team as scientist Jane Godiksen​ celebrated her birthday. Colleagues and friends strung up some decorations in one of the labs, and the kitchen staff continued their excellent work by baking a dessert (ok - we usually get something sweet mid-afternoon, but this was that extra bit tasty).

So here's wishing ​​Jane a happy birthday or, as they say in Norwegian, gratulerer med dagen. ​​​​​​
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July 25
In the Same Boat

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Terje Haugland, instrument operator

Can you tell me a bit about your role on the boat?

We are two people, I am the instrument operator and my colleague is the instrument chief. I do the 12-6 shifts and he does the 6-12, so are supervising the instruments twenty-four hours. Our main job is to make sure everything is running and to try and solve problems. We communicate with upstairs (the captain's bridge).

On this cruise the main instrument is the echosounder, four different frequencies. We also have the CTD (conductivity, temperature and instrument) monitor and the deck unit, an interface box between the computer and the CTD sensor probe downstairs.

What do you like about life at sea?

We work twelve hours, which gives me extra spare time when I get home. I like to work that way: work a lot when I work and then have the time off. I don't like to be tortured by the alarm bell every morning like other people do. Life at sea can be very monotonous, but this way of working suits me well.

Ocean and marine research is a very interesting field, the fish stock assessments. We have different kinds of cruises but I like to go on fishery cruises. ​

July 25
Live and acoustic

​​Last night there was an issue with the trawl net; when it was removed from the water it was significantly torn. This meant a new net, already calibrated, had to be fitted so we could carry on as usual.2015 activity map.jpg

​Where we've been on the cruise so far, with key at bottom

Today saw us arrive in the Shetland Islands to refuel the boat and swap our sea legs for our land legs to look around the capital, Lerwick, for a few hours. Everyone had been greatly anticipating dropping in on the archipelago, and with the sun out in the morning, the journey into the port was a thrilling one. ​​shetland.jpg

​Under scrutiny
As mentioned before, another survey being undertaken by IMR during this trip to sea is one for a large fish of the cod family known as saithe.

Over parts of the survey area, the Johan Hjort has made its way along several transects scanning the depths for the fish, stopping intermittently when the echogram showed larger, redder patches (proportional to a larger fish) that the cruise leader considers of interest. Then a trawl takes place. 'Blind trawls' are also taken where, although there's little of interest being picked up on-screen, the scientists need to be sure nothing is being missed.

But the real-time tracking is only part of the picture. Acoustic readings for the nautical miles of the transect already cruised by the vessel need to be performed. This process – scrutinizing the acoustic data – is carried out twice a day on board by cruise leader Jennifer Devine and IMR instrument technician Jan Erik Nygård using the Large Scale Survey System (LSSS) software co-developed by IMR. Consistency is key here as experts can have different analytical techniques, and a switch of personnel could be reflected in the end data.

JE.jpgOn the computer screen, the backscatter (energy pinged back towards and received by the vessel's echosounder) over the travelled path is displayed as coloured specks and patches. These are the reflections of the sonar waves off the part of the fish of the fish that the instrument detects: their swim bladders, which contain air and are therefore of a different density to the area around. Some blobs are shaped like tiny bananas because of the shapes of their swim bladders, the body parts that the sonar waves bounce off (as well as other reflective objects like the seabed, gas-filled bubbles and gas pockets in plankton and jellyfish; weak sound is also reflected off bones). To the untrained eye a lot of it looks like fuzz, but to the experts it is raw data ready to be picked apart in order to tell one sea species from another. 

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Sound waves from an echosounder bouncing back off an orange roughy, a species which doesn't reflect as strongly due to its swim bladder being full of wax esters rather than gas. The red and blue colours indicate a denser signal whilst blue and yellow a more dispersed one. The arrow here shows the bump of the swim bladder; waves also reflect of the fish's otoliths. Image:  Macaulay, G. J., Hart, A. C., Grimes, P. J., Coombs, R., Barr, R., and Dunford, A. J. 2002. Estimation of the target strength of oreo and associated species. Final Research Report for Ministry of Fisheries Research Project OEO2000/01A Objective 1.​​​ 


Because the screen mirrors how the sea is layered, a stratification that scientists call the water column, it is helpful to understand how this works in practice.

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The echogram sliced into horizontal layers for each water column zone, the very bottom layer is a zoomed in version of the seafloor layer above it. The left scale is water depth, the right the backscatter – amount of pinged back energy – threshold. 


The transects are broken down into clearer-to-see segments of five nautical miles, to historically go back over the cruised area to determine what organisms were in the echosounder's radius around the boat – and their composition. 

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The boat's path, along which the acoustic data is scrutinized


So how to single out saithe from the acoustics? It's a stealthy creature, hard to pick up using underwater sonar, so it's not always an easy task. Telling it apart from other big fish is also tough, a fact not helped by the acoustic 'dead zone' adjacent to the sea floor where demersal fish may be hidden by the echo of the sonar waves off the bottom.

We know saithe is benthopelagic – lives close to the bottom (the benthos) but also venturing into higher waters (pelagic zone). So a range of around 100-200 metres, although it has also been caught in surface tows. To start with the three regions are set on the screen: lower (typically the 10 metres closest to the sea floor), middle (usually pelagic fish and plankton) and upper (usually herring and densest plankton congregations). The backscatter threshold is increased, which filters out the plankton from each region in turn.

In the midwater (pelagic) zone, once the plankton are out, bigger fish that are left  can be selected with the mouse and merged with the demersal layer. The sonar has also picked up lots of young haddock and whiting (known as zero group due to their age) in this zone this year, and these are removed in the scrutinizing process as they're not target species.  


acoustics4.jpgHere's the echogram after plankton has been removed from each of the layers (compare with screenshot above). The peaks in the second red line down indicate where large fish in the middle area have been identified and ringed in order to include them in scrutinizing the bottom layer.


Further work now need to be done in the bottom (demersal) zone, the region of interest. Sometimes there are dense red patches representing Norway pout. At night, as the fish rise from the sea floor and disperse. If this happens, they too can be disregarded along with the pelagic zone. If they're on the seabed, they're left in the layer.

Also, the fish sampled in the catch at a trawl site is vital in determining species composition of the backscatter. Data collected from the fish caught be the trawl can be displayed alongside LSSS, where number of each species caught, total weight, length frequency information, as well as proportion of the backscatter attributed to the main species can be displayed. Looking at this data, as well as the lengths, can help when scrutinizing. 

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The fish by species, total weight and number of individuals, as caught at each of the acoustic trawl stations. 


Further clues to the species composition can be given using the frequency response – the amount of backscatter at each of the four acoustic frequencies used on the vessel. When a dense school in the bottom layer could be either herring or Norway pout, for instance, a ring can be drawn around the patch to find out which, as the species have very different responses. This can also help for identifying saithe.

Using the data from the trawls carried out within a certain radius coupled with the acoustic information, we then can work out the proportions of backscatter that should 'belong' with each species.

July 23
In the same boat

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Simen de Lange, developer at IMR

What's your role on this survey?

I'm on this cruise to observe and get some experience on how people are measuring, registering and taking samples of fish in order to make new software to do this.

What's the idea with the new software?

You take a catch, a lot of fish, you take length, weight, sexual maturity staging and register them in a database. The system today actually works quite well, but there are some quirks. You could, for example, accidentally delete everything and it's permanently gone. This new software eliminates that possibility. Also you might get some on-screen help text about what you're supposed to do. If you have a question about sexual maturity staging of gonads – has it spawned? Will is spawn? – you could get pictures on the screen showing you different stages.

What have you learned on this cruise?

It's been quite different to what I thought. I would make something not as useful if I wasn't on this cruise.

Any challenges being on the cruise?

I miss my cat and my girlfriend! A little bit of seasickness but nothing serious. ​

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Raymond Veivåg (left) – catering assistant; Vermund Aase (right) – chief steward

What's your role on the ship?​

Vermund: I buy all the stuff you need for a cruise and all the economics side of things – everything from the toothpicks to the meat. I make sure everyone has a comfortable cruise. I also have to prepare all the meals. The ship can take up to 39 people, that's quite a lot.

Raymond: I make sure the ship is clean and assist with the food and meals.

Biggest challenge?

Vermund: When you have bad weather for a long time, especially in the winter on the Barents Sea and Norwegian Sea

Raymond: To make and serve the food during bad weather. You can get bad weather in the North Sea also.

Fondest memory at sea?

Raymond: you could write a book!

Valmund: So many nice memories. We have a nice place to work

Raymond: we've been at sea for 35 years so there are a lot of stories

Valmund: of course most of the stories are secrets. You have two lives – one at sea and one as a private person back home, as a family man. Two very different lives.

Raymond: I'm not sure if it's a healthy life but it's a life. It's become a lifestyle. 

July 22
Stage 6 – Digital digest

​"If we don't manage this resource, we will be left with a diet of jellyfish and plankton stew." - Daniel Pauly

Update: We're now on a northern path, edging ever closer to the Shetland Islands and our westernmost survey rectangles. Yesterday we picked up both IBTS and saithe trawls, although we did experience a small problem with the trawl net at one station. Upon winding the net in, the crew discovered that the cod end, the slimmer enclosure at the end of the netting in which the fish bunch, had broken whilst in the water. Although several larger fish were present, the damage meant that any smaller fish that had entered the GOV would have wriggled free, rendering the trawl invalid. With the catch now unrepresentative, we had to try again.

One interesting organism – or parts of an organism – was found in the catch yesterday, puzzling the scientists for a short while. It came in the form of some glutinous, jellybean-like specimens. After some speculation and research they were found to be hagfish​ eggs. 

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A numbers game
We'll now look at the stage in the process where the handling of the physical fish makes way for the handling of the numbers that represent them. The fish have been sorted, sampled​ and (in some cases) sliced, the gloves and overalls are off and the wet lab has been cleaned of fishy residue.

The team of scientists on the shift then sit down to store and process their findings on a computer. 

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First the length and weight data from the three electronic measuring boards in the lab is automatically fed into the system. This arrives with metadata from the bridge – the control deck – on the sampling station number, depth and times of the trawl, the ICES rectangle we're positioned in, trawl net mouth opening and length of wire, amongst other things. Stored together, all this information is logged for the current station (number 2421), sitting alongside the data from the 140 other stations called at since the survey started out back at the end of June.

Once the data has been uploaded, it is pooled in one table, categorised by species in the sample with various codes denoting the type of sample taken and number in the sample, fish lengths, weights of the ones that are length measured, and so on. Any age data, obtained from the otolith readings, is added later.

Other keys describe the units of weight and of length and the way the measurement has been taken. For most fish species this is from tip of snout to end of caudal fin. For octopuses and squids (cephalopods) it is the length of their mantle, or body minus the tentacles. For crustaceans the size of their shell (carapace). For the former that's because the tentacles tend to contract and for the latter because the hard shell is unchanging, both offering a better indication of size. Details of crustaceans and other seafloor non-fish can be entered into the computer manually at the end. 

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This process is the same for both the surveys carried out on the Johan Hjort. However, for the IBTS and the saithe survey, two separate calculations are performed due to a key difference between them: that is, that the IBTS catch is organized into species whereas for the saithe, after the larger fish have been picked out,  a subsample of a mixture of the smaller species (such as Norway pout,  blue whiting and silver cod)   is taken. This is to give a representation of the weight of each species in the catch as well as to save time between trawls. 

For the IBTS, the catch often yields a lot of Norway pout, which when sorted can result in often numerous baskets (sometimes as many as 15!) . Although these are separated, counting them all would take forever and wouldn't make the data any more accurate.  

So, to work out the amount of, say, Norway pout in the catch, the scientists take the total weight of all baskets of the species (let's say 20 kilogrammes), multiply it by the number of pout in the sample (here, 100, as that's the maximum number that can be sampled – and there are way more than that) and then divide by the weight of the sample (let's say 5 kilos). So 20 x 100, over five – a sum that gives us 400, meaning there were 400 in the original catch.

If there was a notable size discrepancy in the pout (enough to get an adequate representation), then they might be split into two samples – big and small haddock for example.​

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Finally, the data is checked against that from all other stations for incongruities, with some entries fixed now and some later. Notes can also be made on the trawl. Was it initiated because of an echogram (for the saithe)? Did it pass by without any problems? Was there any gear damage? Was it a blind trawl? Or, just like ours yesterday when the cod end came undone, did it not fish correctly?

Everything is mapped and even the smallest detail could prove important when the data is processed further and cleaned by IMR later.

In the meantime, this batch is exported to the upper deck of the Johan Hjort to be turned into graphs and maps that show how the lengths of fish are distributed across the survey area. 

July 21
In the same boat

​​​​​​​​Inger Marie Beck​, IMR, ​​​whose areas of expertise include diet analysis for demersal fish, benthic habitat and taxonomy, and fish diet.

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How're things going on the cruise?
Things are going fine. The catches aren't as big as we're used to, but they're telling us a lot. Earlier we used to trawl for longer, but the design is different. ​Fifteen minutes gives you enough. It gives you the impression that you want and​ enough data to tell you something over one quarter (of the survey, this part being quarter 3).

What's your favourite thing about being at sea?

It's very special to be on the sea because you're like a big family. Everybody's very tightly connected to each other. You're not as distant as you are on land.

What's the biggest challenge about being away on a survey?

Being away from children, many of my colleagues have them, and from family and friends. But we're lucky at the institute if you have small children at home – you can participate in shorter cruises, one week or ten days, for example. It's ok like that. ​Also in summer there can often be fog on the ocean and people are at home having a nice time.

July 21
Testing the waters

​“Catch a wave, and you’re sitting on top of the world.” ​– The Beach Boys​​.

Yesterday, Monday, was spent cruising southwards again, picking up both IBTS trawls and saithe acoustic sampling on the way. Progress seems to be good – a small trawl net deficiency at one station aside – and I'll update the blog with a cruise map tomorrow.

The big news was that a whale was spotted breaching by the captain. "It doesn't happen very often here," he explained to me later. "We see a lot in the Barents Sea."  

​​​Guding lights
Of course steering and navigating the Johan Hjort is more than a step in a process, it's a round-the-clock endeavour. From the control room at the top of the vessel, known as the bridge, captain John Gerhard Aasen pulls the strings at a desk which holds a suite of screens, panels and buttons. Around the room, which provides a panoramic of the sea, there is also communications equipment, and chairs on either wing from which he can further run the boat. With the Johan Hjort on the water for​​​​​​ 320 days of the year, only the finest, most reliable equipment will do.

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The focal point of the operation is a high-tech map, which is dotted with geographical and physical information, including the delimited rectangles in which the trawls are conducted and all historical trawl sites mapped by the boat. Using this, John Gerhard can guide the boat to the paths that the vessel will tow down with a few mouse manoeuvres. He can also call up a projected depth range for the path. Other information shown on the map includes oil and gas pipes, oil rigs and oceanographic features such as deeper and shallower water. In the centre is the boat itself, the position visible though GPS.

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John Gerhard has spent four years in charge of the Johan Hjort and has captained many other vessels mostly in the Barents Sea ("The biggest difference between the North and Barents seas is that there is more traffic here. More oil rigs, oil pipes, gas lines and things like that.").

He explains to me how the trawl is deployed at each site by setting the cable that links the net to the back of the boat into motion. A monitor relays information on the length of the cable and an echosounder shows the trawl nets depth. When bringing it in, he stops the mechanism with 50 metres to spare so that the crew on deck can finish at their own speed (the net sometimes gets tangled towards the end so it helps if they can control the movement of the cable). Once the trawl is in, he gives the green light for the parallel process, the CTD reading.​

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Sound of the CTD

Alongside the fish-catching part of each trawl, the local environment is also tested for a range of variables, with the seawater being sampled at each station is for its conductivity (C​​) and temperature (T) relative to its depth (D). From the conductivity reading, the water's​​ salinity can then be deduced, and salinity and ​​temperature data can be combined to give the density.

The instrument that takes the measurements is called a CTD (after the things it's monitoring) – a barrel-shaped construction called a rosette which is armed with a temperature and pressure sensors, weights to help submerge it, a remotely-operated cylindrical tube which captures a water sample, and a pump which flushes water through to measure conductivity.

Once the trawl net comes in, the captain gives the go-ahead and the depth to which to lower the gadget. This particular one, manned by deckhand Anders Strønen, is going in at 150 metres and will stop five metres from the seafloor. Here the water is more stable.

The process then goes as follows:

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First, a panel large enough to drive a van through is opened on the side of the boat.

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It is then lowered to the required depths. Though here this time, because the CTD happens so quickly after a trawl, the water around is usually carpeted by seabirds waiting for what they think is a​ feeding. 

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It is then underwater for ​​about five minutes.​​

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Then returned to its resting position. The data is delivered automatically to a computer up in the instrument room and stored on a database.

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The tube containing the seawater sample is decanted into a glass bottle.

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Bottles from each station are labelled and boxed up for instrument calibration purposes.​

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The rosette can actually hold up to 12 of these water cylinders. During the hydrographic section of the IBTS - the final leg that will take place after I leave the vessel - experts will analyse the water within these for such things as nutrients and chlorophyll. When the rosette is fully stocked, each of these tubes samples water at a different depth during its ascent from the depths. 

All this hydrographic and environmental information mapped over time provides a valuable record of the conditions within which marine organisms live, offering trends and the ability to produce temperature maps across the surveyed area, amongst other things. 

​I will cover how this information is used by ICES in a later post.

July 21
Creature feature – Norway pout

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We've been hoisting basket-loads of a diminutive fish called Norway pout in the IBTS nets since the start of the trip. 

A member of the cod family, the species is marked by a lower lip that juts out slightly beyond the top one (hence its name?). It doesn't have a long lifespan – around four to five years tops – and spends its days in close proximity to the seabed at a range of depths. It has, however, been observed rising from the bottom during the night.

Norway pout is fished throughout north-eastern Atlantic waters, from the Channel to Iceland and along the Norwegian coastline to the lower western corner of the Barents. The heart of its distribution lies midway between the Shetland Islands and the edge of Norway, which means the Johan Hjort is cruising across prime pout territory.

Humans aren't big eaters of these little fish, but both the ecosystem and the economy have a sizeable reliance on it. In the sea it is a key link in the food chain as prey for cod, hake and monkfish amongst others, whilst once caught it is processed into fishmeal for farmed species like salmon and also into fish oil.

To look at the graph below (from ICES) of Norway pout catches since the 1980s is to get a good idea of how they've risen and fallen over the decades, at times quite dramatically. From virtually nothing in the 60s to literally tens of thousands of tonnes tonnes in the mid-70s, the number dipped again by the mid-80s, fluctuating from then until a severe decline in recent years. The North Sea fishery was even closed a few times between 2005-2007.

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​Being a short-lived species, ​the population dynamic can change pretty quickly​​, and with so many species calling pout dinner, predation from year to year can also affect the stock. To its advantage, the spwaning ability of the female pout​, ​420-980 eggs per gram​ of body weight, helps the stocks to recover under the right management conditions. 

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Squat lobster
Fishing for data ​is a blog that documents the Norwegian third quarter leg of the ICES-coordinated International Bottom Trawl Survey (IBTS) in the North Sea. From aging fish to recording environmental conditions, the data collected on research missions of these types represent the beginning of the ICES story.

Simon Cooper is a communications assistant at the ICES Secretariat, who joined the IBTS cruise from the 15th - 26th July.​​

Photo: A squat lobster being measured​; Sebastian Valanko