The boat lurches down the rolling waves, and heaves back up. “I thought it would be worse,” says skipper Emma Burgess, smiling at my ashen face from behind the wheel. “This isn’t bad at all.”

I head below. It’s the worst place to be when sea-sickness strikes, but my attempt to travel without vomiting on a sailing boat through the Sea of the Hebrides is over. I steady my footing in the cabin and gulp down two Stugeron tablets, then dash back on deck where I watch the waves coming, the best way to fight the nausea.

An hour later the tablets seem to kick in and I’m fine despite the rolling action.

I take my turn on lookout duty, clipping myself to the deck to ensure I don’t fall off. I scan the sea for whales, dolphins, porpoises, seals and creel buoys. It’s what we’re here to do.

We’re on the Silurian, the 61ft sailing ketch at the heart of the work of the Hebridean Whale and Dolphin Trust, to carry out research into the whales and dolphins – cetaceans – and other wildlife in the seas off the west coast.

More than 20 species of whales, dolphins and porpoises are regularly seen plus common seals, and we have a third of the world population of the larger grey seals. But they are under threat: from noise, pollution, discarded fishing gear and even tourism. A Cuvier’s beaked whale stranded on Skye in 2015 died with its belly full of plastic bags. Over a hundred of the deep-diving whales were found dead last summer in the north Atlantic, most of them in Scotland. Military sonar is a strong suspect.

Entanglements in creel ropes and other equipment is a regular problem for cetaceans and seals, with a dead whale in Scrabster recently tangled in creel gear from Nova Scotia. Last but not least, marine mammals are victims of their own popularity. Tourists crowd onto boats to see them, and tour operators are under pressure to provide ever-closer encounters. Scottish Wildlife Trust has called for tougher controls on tourism operations.

The data from the Silurian – collected in 144,000 hours of volunteer work on more than 200 trips on the west coast – is crucial. The Trust’s science officer Lauren Hartny-Mills gives an example: having hard facts enables it and other agencies in the Scottish Entanglement Alliance to engage with fishing operators over why entanglements happen and their impacts, and come up with solutions.

She says: “No entanglement is intentional and it’s really upsetting for the fishers who find these animals in distress in their gear, but they also lose money from cutting animals free and lost fishing time.”

Survey information is used to find where marine animals and fishing gear clash, and photo data collected on surveys can give clues to what injuries cetaceans suffer at the hands of man-made objects and machinery.

And the data is particularly important because Government consultations are afoot for four new Marine Protected Areas in Scottish waters, three off the west coast, including a 10,000 sq km one in the Sea of the Hebrides.

Data from the Silurian has been key in defining that last MPA and a smaller one off the north east coast of Lewis. HWDT information on the movements of minke whales and Risso’s dolphins and other creatures will help the Scottish Government set the MPA rules under which fishing, tourism and development are regulated.

After heading west out of Tobermory in the early morning, we face the full force of the weather as we turn south-west into the sea lane between Mull, Coll and Tiree. With me on the boat are volunteers Jenny Hampson, based on Mull, and Andy Tait, who’s from the north-east of England but spends much of his time on the island. The rest of the six-strong volunteer complement is made up of young undergraduates, mainly marine science students, who combine knowledge of the sea environment and its problems with an enthusiasm and delight in the wildlife.

Mancunian Hampson is studying for a masters in marine mammal science at St Andrews, and was a full-time volunteer for the trust for nine months. She functions like an extra member of staff, knowing the routines and the rules from helping out on previous trips.

As the rolling eases near the dramatic little Treshnish Isles, I head below again where she’s at work. Information on species, direction of travel, distance and behaviour of any animal spotted is yelled down from the watch team on the mast, and she shows me how it’s put into a database and turned into statistics.

In the rough conditions and rain it’s much harder to see anything on the surface, and that’s where the hydrophone towed behind the boat comes into its own.

Hampson explains it collects the sounds of porpoises, which are plotted into the database. It also shows up the whistles of dolphins, the snapping sounds made by shrimps, and things such as the acoustic deterrent devices which blare out sound to drive seals away from fish farms.

“I wanted to do this since I was about five – I have always been one of those whale nuts,” says Hampson.

Tait has been a volunteer for HWDT since it started in 1994. On his trips he’s seen orca, four different species of dolphin as well as masses of other wildlife – he’s good on bird identification too.

“I do it all because I love wildlife. This is what I live for now since I retired,” he says.

We’re on only the third of a new series of winter-months surveys by Silurian. In the past she has normally sailed from April to October only, taking paying volunteers on trips of up to 12 days across the Hebrides, counting the mammals as they go. That has built up a wealth of data but more information is needed.

This trip is paid for out of a grant from the Scottish Government’s wildlife agency Scottish Natural Heritage (SNH) – HWDT will get a total of around £112,000 over three years year from SNH for its survey work – and these winter surveys are different, drawing on local volunteers to do similar work for shorter periods, at short notice, as weather windows allow.

Volunteers go free on the three-day trips but they have to put up with the lurching winter seas, and sometimes worse: on January’s trip they were chipping ice off the deck. More winter surveys will follow over the next two years, giving scientists the first proper picture of what west coast cetacean and seal populations are like in winter and how they behave.

We turn east, and my second night aboard is spent moored in a small cove on the north side of Ulva, off the coast of Mull, whose inhabitants famously won more than £4 million from the Scottish Government to buy the island and tempt people to repopulate it.

From here it looks bleak and inhospitable, and we scrap a plan for a run ashore in favour of sketching, board games and chat before an early night. Some of the students sit drawing simple outlines of marine mammals, trying to capture the essence of the creatures, the movement that makes their massive forms so graceful.

Everyone helps with cooking and clearing up, with Burgess and first mate Brian Condon giving a gentle guiding hand.

The next day we retrace our steps, and as we turn back into the Sound of Mull, and get the stiff south-west wind behind us, the engine is switched off and we come under pure sail.

Four oyster catchers pass, much faster than the boat, bouncing in the wind as they dip and flit. The light, down into the sound and in towards the folded land, is shifting in the heaps of mist and cloud. A rag of blue sky slips away, the brightness briefly lighting the toe of the ness ahead.

On deck the volunteers are concentrating hard on the count. We have seen seals and harbour porpoise, but so far none of the larger marine mammals. However hard you’re looking, though, it’s difficult not to be distracted by the beauty around you.

Burgess tells me this interplay of light and sea is what she loves. “People ask me if I get bored with just sea and sky to look at. But even when you’re right out at sea with no land in sight, it changes all the time – it’s fascinating.”

As skipper and boat manager she commands her one crew member, decides where and how we travel, looks after motley volunteers including myself, and helps ensure the vital survey work is done properly. As she steers the boat she tells me she “fell back into the west coast of Scotland” and became skipper a year ago after working as first mate on Silurian then as a diver and sailor around the world.

A Mull native who studied marine biology, she’s from a fishing family and has an ease born of years of familiarity with the boat, the sea and the whole system that keeps us alive in this alien environment. She also chips in on occasion with a reality check about people needing to make a living when volunteer enthusiasm for marine conservation bubbles over.

Working the Silurian is a different challenge to other sailing jobs. The science comes first and that means travelling in straight lines – transects – at seven knots, so consistent counts of animals and objects can be made.

“We try to cover as many different areas as possible that we haven’t done before but the weather quite often doesn’t let us go exactly where we want to go,” Burgess says. “You also have to think about where you can anchor on the evening so people get a good night’s rest so they can carry on working the next day.

“Then you have the tides, which also dictate where we’re going, there are massive tidal streams around a lot of the islands. “It’s a ever-ending puzzle of trying to work out what’s going to be the most effective way of managing to survey the areas we’re going to cover.”

The boat was built in Seattle in 1981 and has led a colourful career: in the 1990s it was picked up by the US Coastguard off the coast of Florida and impounded for smuggling cocaine from Columbia. A few years later she was used by a team filming for the first Blue Planet documentary for the BBC, before being acquired by the Trust in 2002.

Burgess says Silurian’s considerable weight allows the vessel to batter through much of the bad weather. A refit last year smartened her rigging up, and the combination of sails and engine means she can make the best of any weather.

Our third evening is spent moored in the small bay north-west of Castle Duart on the heel of Mull towards Oban. The constant drizzle that soaked the last watch of volunteers has stopped as I step out on deck in the early evening with Becky Dudley, HWDT’s marine biodiversity officer.

We watch fascinated as the moon slides in and out of cloud, throwing silver onto flat dusk water. As we talk a common seal approaches the boat, drawing smiles and coos from the volunteers.

Dudley admits to her personal devotion to whales and dolphins: it started with a cetacean-themed quilt-cover as a child. But, she says the science is what matters, and decision-making using hard data is essential: “It’s really important for instance that the boundaries and what happens in the MPAs aren’t just based on guesswork. You want solid scientific data to show where the animals are, where they’re not, how the populations are doing within that area and how many species are using that area.”

Later I ask the Trust’s director Alison Lomax why it is that people’s unscientific, almost anthropomorphic ideas, draw them towards cetaceans.

“With whales and dolphins there’s certainly a connection that those types of animals allow you to make,” she says “These animals are so mysterious, we are still learning so much about them, and yet there are so many similarities between us and them in terms of our biology and parts of our behaviour.

“For me it’s that key moment where you get just that glimpse of a whale or a dolphin and your world and theirs meets – that is something that is quite inspiring, and it brings tears to some people’s eyes.”

At Castle Duart we are up early next day for a full day’s work before we head back to port. The boat chugs into Loch Linnhe, flat water welcome on the balance and legs, but it’s dull compared to the wave-crashing, swell-riding trip to Ulva and back. There are more seals and creels, but not much sign of cetaceans as we head up and around Lismore, then back south around Morven.

Then, by the scar of the huge Glensanda quarry, there’s a wave of excitement. Someone has spotted a common dolphin, the first of the trip after three days, gently rising with a graceful arch of the back, and sliding back below the ruffled water. Every time we think we’ve seen the last of it, it pops up again, close enough and high enough to see the distinctive cream-coloured patches on its sides.

Cameras click, and it is recorded in the data base: species, behaviour, direction of travel, bearing from the boat, another small case to add to the thousands logged by the Silurian.

Dudley, however, looks concerned. She plans to report the sighting to British Divers Marine Life Rescue (BDMLR). The animal is alone, which is unusual; its calm, smooth movement is a bit too gentle for a creature often seen leaping and twisting around. There could be something amiss, and local observers from BDMLR can keep an eye out in case the animal is injured or unwell, and ends up stranded.

Later she tells me there’s been no response to her call, indicating the animal has not been spotted again or got into trouble, but it’s another indication of the care HWDT staff take of these animals. The survey work can be enjoyable, there can be glorious moments and exciting sightings, but working on the Silurian, and volunteering on it, is no easy task, as the seasickness taught me. That the Trust, staff and volunteers take this task on, helps not only the animals they care for but the whole marine ecosystem. Whatever drives them, we’re better off for it.

PROTECTION – OR JUST PAPER PARKS?

Four new Marine Protected Areas are proposed by the Scottish Government: the 10,000 sq km Sea of the Hebrides MPA; the smaller North East Lewis and nearby Shiant East Bank MPAs; and the Southern Trench MPA off the Aberdeenshire and Moray coasts.

All are supposed to protect a range of animals and features, but data collected by HWDT’s teams will be crucial in protecting Minke whales and basking sharks in the Sea of the Hebrides, and Risso’s dolphins off Lewis.

The Scottish Government is consulting on how they should be defined, and designation does mean some constraints on development. After that there will be lengthy debate over “management measures”, controlling activity with the MPA areas, with the battle lines likely to be drawn between conservation campaigners and the fishing industry.

The consultation document suggests a cost of £14m to the oil and gas, power transmission and fishing industries from the strictest likely control measures, although it says the benefits to the economy could be far greater.

Nick Underwood of Scottish conservation charity Open Seas fears the MPAs will be designated but won’t have the rules in place needed to regulate damaging activity. “These sites are already long delayed – there have been worrying delays in the implementation of these MPAs,” he says. “These sites need to be designated as soon as possible with meaningful management. Until that management is in place these are just going to be paper parks.”

Elena Balestri, science policy officer for the Scottish Fishermen's Federation, says: “Every level of protection needs to be based on scientific evidence. As long as the fishing industry is kept in the loop and in the process and as long as the views and experience of the fishermen and the overlap between protection and the fishing grounds is minimised, then we are in favour of protection of cetaceans and marine mammals.”

A Scottish Government spokesperson said: “Once designated, these sites will receive new levels of protection which mean decision makers have a legal responsibility to consider the effects of activities on the sites and features.”