As we chug out of the little harbour, the view of russet hills and the blue peak of Beinn Alligin is distractingly gorgeous, but it's forgotten as soon as we look down through the glass hull at the teeming life below. Straight away we are soaring over settlements and busy highways. Striking out over the flat, sandy floor of the loch, a young brown crab scuttles purposefully towards who knows what, narrowly missing two more industrious souls coming the other way, like traffic passing at a crossroads. Occasionally there are flashes of silver as shoals of herring slide past.
Then a rocky outcrop looms out of the sand like a range of low hills and the demographic changes. Huge, fat, orange starfish lounge about like sunbathers at their weekend retreats, one leg slung over a rock, another trailing in the water. Dozens of sea urchins colonise fissures in the rock, their perfect round heads alabaster white with delicate spines of pink, like the domes of an exotic hotel.
Leaving the rocky cliffs behind, we move out again over the open plain where grazing "herds" of hermit crabs are dotted all over the seabed and the odd flat fish creeps through the sand. Beyond them, we come to a seaweedy length of rope drifting in the swell, a condominium for invertebrates, where a colony of plumose anemones – orange cylinders with a shock of feather-duster tentacles at the end – have taken up residence. A spider crab, comically festooned with barnacles and tufts of seaweed, is edging like a cat burglar up the rope.
Holmes shares his encyclopedic knowledge in digestible titbits. Did we know that hermit crabs can live for 30 years? That stressed starfish sometimes shed a leg?
We see a swimming crab shoot past like a mechanical bath toy, its flippers flapping furiously, and watch scallops feeding, their orange frills on show. There's a cushion star, Holmes points out – it has little legs and a much fatter body than other starfish – and that fish over there with the tiger stripes is a wrasse. We are utterly absorbed. Seventy per cent of life exists in the ocean, Holmes remarks, and people are often shocked by how much there is to see. There are around 8000 species in the seas around Scotland and new ones are still being discovered, but many are completely unknown to Scotland's human inhabitants, particularly deep-water species. Further out and deeper down in Loch Gairloch, for instance, there are maerl beds, areas of exotic-looking hard purple-red seaweed which are crucially important nursery habitats for juvenile fish, young scallops and numerous other species, including mussels, clams, oysters, urchins, sea cucumbers, anemones and worms. Loch Gairloch also has precious eelgrass beds, important for sea horses.
Like many seabed habitats, eel grass and slow-growing maerl beds can be damaged by dredging and bottom-trawling. The loch has been closed to trawlers and dredgers under fishing regulations since 1984, but in Loch Ewe to the north, locals say the maerl has been degraded over the past 20 years by fishing gear.
To protect the ecosystem – maerl, fish, shellfish, marine birds and mammals – that so much of their economy relies upon, local people are bidding to make Gairloch and Wester Loch Ewe a Marine Protected Area (MPA), where the marine habitat, wildlife and geology will receive special protection. A list of proposed MPAs – put together for inshore waters by Scottish Natural Heritage (SNH) and offshore waters by the Joint Nature Conservation Committee (JNCC) – will go before the Scottish Parliament later this month before more detailed proposals go out for consultation early next summer.
The list is awaited with a mixture of excitement and anxiety by conservationists and those working in and around Scotland's seas, many of whom are worried about damage from fishing and other activities.
Peter Cunningham, a biologist with Wester Ross Fisheries Trust, who is leading the bid for the Gairloch and Wester Loch Ewe MPA, believes for instance that maerl beds should be protected wherever they occur. RSPB Scotland wants MPAs designated for seabirds. Meanwhile, Calum Duncan of the Marine Conservation Society in Scotland (MCS) worries that almost all of Scotland's seabed habitats to the continental shelf and beyond, particularly sedimentary and deep-water types, are giving cause for concern and/or are in a state of decline, highlighting the evidence of Scotland's Marine Atlas 2011, a Scottish Government assessment of our seas.
"The developing network of MPAs must not only protect the best of what's left of the seabed but also help recover a sufficient extent of the rest to help get our seas back to health," Duncan says.
For the Government, though, conservation is not the only consideration. Ministers must also weigh up social and economic requirements, says Susan Davies, director of policy and advice for SNH. "Some of the economic interests we have – such as agriculture, tourism and renewables – sit alongside the conservation ones," she notes. "It's about having the right plan in the right place."
Bertie Armstrong, chief executive of the Scottish Fishermen's Federation, notes that 200 areas of the sea have been closed to fishing this year and that a lot of the features protected by MPAs are not targeted by fishermen anyway. He adds: "The fishing industry has no problem with MPAs if they pass the test of why they are there, how will we monitor them, and if they don't work, how will we get out of them."
As for maerl beds, in some places they will be proposed as "MPA-protected features", but not all will receive this designation (though there are other ways they might be protected – MPAs are one among a range of tools for managing the seas).
In the eight years Richard Holmes has been observing life in Loch Gairloch, he has seen some changes. There are fewer green plankton blooms than he used to see, as well as fewer oystercatchers and terns around. This personal experience reflects the survey evidence: arctic terns in Scotland have declined by 72% in the past 25 years, according to a recent SNH study, while oystercatcher numbers have dropped by 14% in the past decade, according to the RSPB's report The State Of UK Birds.
The system of MPAs, Holmes hopes, will make people more aware of what lives in the water and that it is worth protecting.
So what is out there? Drained of its water, the seabed would be a place of mighty mountains and dramatic glens. Underwater Scotland is populated by many creatures that are so colourful they look like they've blown in from the Caribbean. Some, like squat lobsters, which are abundant around the west coast, are full of anthropomorphic charm, with their big eyes and long pincers.
Several species of Scotland's marine wildlife, such as otters, minke whales and dolphins, are well known, but many are not, including important species that are under threat. It's time to meet the neighbours.
Yes, the ones TV nature programmes show laying their eggs on far-flung beaches. The world's largest turtle and fastest-moving reptile (they can reach 22mph in the water), these critically endangered animals are seasonal visitors, says Calum Duncan. "They are a genuinely endemic part of our marine fauna. They are the world's most widely distributed reptile and come here because their favourite food is jellyfish, which is abundant in sub-polar and temperate waters."
Where found: west coast and Northern Isles.
The second largest living fish, measuring 6-8m in length, these gentle creatures filter plankton through their open mouths and have a dorsal fin more than a metre high. Although protected, feeding close to the surface makes them vulnerable to getting caught in fishing nets or being hit by jet-skis or boats. Duncan has encountered basking sharks twice while diving, off Rum and Skye. The first time, one passed under his feet. "It was this elephantine beast, a huge grey creature. It had almost comically tiny eyes and a bulbous nose. It was as long as a minibus and took a couple of seconds to pass."
Where found: according to SNH, hotspots in the outer Firth of Clyde; Gunna Sound, between Coll and Tiree; and around the rocky islet of Hyskeir, south-west of Canna; occasionally seen off the east coast.
A classic shark, with small, razor-sharp teeth, the tope or school shark grows to up to 2m and can live to be 55 years old. Vulnerable globally to being fished for its fin and becoming bycatch, it does not mature until 10 years old, so where numbers drop, they are slow to recover. It is against the law to land a tope in Scottish waters.
Where found: though more common off the west coast, a mackerel fisherman filmed one off Methil in the Firth of Forth this summer, where they were wiped out by overfishing 40 years ago.
Northern feather star
Beautiful, fragile, balletic creatures which are mainly to be seen attached to rocks and swaying in the swell, filtering food from the water with their 10 willowy arms, but can perform a graceful "dance", swimming from one place to another by flicking their long arms. They come in various colours and are usually found in deep water, but uniquely in Scotland, occur in shallow sea lochs. Listed as a "priority marine feature" by SNH and the JNCC, meaning they are a target of conservation efforts.
Where found: west coast including in the Minch, around Skye and in Loch Sunart; also around Shetland. A video of a dancing northern feather star is at snh.org.uk.
A spiky, vivid purple pink seaweed which hardens with lime deposits over time, maerl carpets the seabed in places creating important shelter for many juveline creatures. A priority marine feature.
Where found: the Sound of Barra; sea lochs of the west coast.
A jellyfish with a stalk and funnel coloured green or red, like a sort of translucent marine orchid, it is found attached to seagrasses in shallow areas.
Where found: west coast; Orkney and Shetland.
Cold water coral
Formed at depths of between 80m and 3000m, Britain's only reef-forming coral, lophelia pertusa, looks like the frosted branches of trees in winter. Usually found in deep water, in 2003 a 100sq km area was found in shallower waters near Mingulay in the Outer Hebrides which has been growing for at least 5000 years; it supports more than 350 species. The coral is badly damaged by deep water trawling and oil exploration, and takes hundreds of years to recover. A priority marine feature. Find out more at lophelia.org.
Where found: north-east Atlantic; important bed off Mingulay, south of Barra.
Tall sea pens
A relative of corals, these native Scottish animals are found in deep mud and stand proud of the seabed, as tall as a person. They trap plankton. Calum Duncan, who has dived among them, says: "The first time I saw them it was 20m down in a sea loch and quite dark. There was this ghostly white sinewy forest coming out of the inky depths. It was eerie but I felt so privileged. They lean in the currents and are quite beautiful in their own way." Threatened by trawling.
Where found: Fladen Ground in the North Sea; sea lochs such as Loch Nevis.
Jewel and fireworks anemones
Neon-lit jewel anemones that light up the deep in colours such as electric green, pink and purple creating spectacular sheets below the kelp line on exposed underwater cliffs. They are common around the west coast. Fireworks anemones, meanwhile, are Britain's biggest anemone. They live in a tube in the mud up to 1m deep with a crown of tentacles like a burst of fireworks on top. A priority for conservation.
Where found: west coast.
A summer tourist more typical in tropical waters that rocks up occasionally off the west coast for the jellyfish. The biggest bony fish in the world, it weighs one metric tonne. Odd-looking, with a frilled skirt of cartilage instead of a tail fin and very small pectoral fins, it tends to be seen basking on its side. Its presence here may be due to rising sea temperatures.
Where found: off the west coast; one was filmed off Eigg in 2010.
Flameshells, quahogs, horse mussels and fan mussels
Scotland has a number of important bivalves (molluscs with a hinged shell), some highly exotic-looking, which are declining and vulnerable to dredging and bottom-trawling. Some, like horse mussels and flameshells, form reefs that stabilise the sea floor, creating habitats for young fish. All are subject to conservation efforts.
Flameshells, with their fringe of orange tentacles and ability to shoot around by opening and closing, look like the Muppets of the sea. Threatened and declining, they build nests by gathering bits of shell and small stones.
Where found: sea lochs like Carron, Broom, Sunart and Creran; Orkney.
The ocean quahog may not look much with its rather plain grey shell, but with a 400-year lifespan it is a contender for world's longest lived animal.
Where found: all around Scotland.
Horse mussels can grow to 20cm. A 450-hectare bed was found near Noss Head, Caithness, during surveys by a power company; it is likely to get protection under an MPA. So is a vitally important colony of fan mussels discovered in the Sound of Canna in 2009. At 30cm, the fan mussel is the king of British seashells. It has a pointed end, buries deep into sediment and leaves the wider part exposed to filter food from the water. Duncan says: "They are extremely rare. Until two years ago, there were only thought to be two individuals left."
This blue and orange fish looks like it belongs on tropical seas, but is in fact found in high numbers in inshore Scottish waters.
Where found: around Scotland, particularly in kelp forests.
This rare but giant type of ray can grow to nearly 3m across. Once found in abundance off Scotland but now so rare worldwide it is listed as critically endangered.
Where found: west coast.