Such mass strandings as those of pilot whales in Scotland and Florida last week address us directly. The sight of dozens of helpless whales out of water, gasping for breath, bowed down by their own weight, seems an all-too powerful emblem of our disconnection from the natural world. To be stranded is to be abandoned, a symbol of our own carelessness. Indeed, these news stories take on a symbolism beyond their awful reality, as parables of morbid fascination, as if their victims had been selected for some terrible experiment.

In Iris Murdoch's strange, Booker-prize winning novel of 1978, The Sea, The Sea, the protagonist, Charles Arrowby's cousin James informs him: "The sea is not all that clean …. Did you know that dolphins sometimes commit suicide by leaping onto the land because they're so tormented by parasites?" To which Charles replies, "I wish you hadn't told me that. Dolphins are such good beasts. So even they have their attendant demons."

In fact, the causes of these events are multiple, and conflicting. Pilot whales, like other toothed cetaceans (dolphins among them) naturally follow one another; if one animal is sick, it may head for shallow water so that it doesn't drown, and its comrades follow it. Anomalies in magnetic paths, laid down in the sea bed, may lead the cetaceans into dead ends. Solar flares, immune systems compromised by heavy metals and, most recently, military and commercial sonar have all been blamed.

We might not know the cause, but the effect is plaintively clear. In unusually large mass strandings of common dolphin in Cape Cod earlier this year, rescuers discovered that the animals became less stressed if they were placed side by side. Intensely social, their only consolation was each other.

What is this vexed relationship between human and natural history? Why are we so drawn to the plight of the whale? One reason is that we share the same physiology. I recently attended the dissection of a harbour porpoise at the Zoological Society of London. In the basement laboratory, I watched as Rob Deaville cut through its blubber like a sushi chef.

I thought I was going to be sick. In fact, as Rob deconstructed the animal before my eyes, I was amazed at how like us it was; every organ echoed ours; even the animal's size evoked our mammalian kinship. (The animal also turned out to have been murdered by bottlenose dolphins in Cardigan Bay – a story which rather undermines the received notion of an ever-smiling Flipper).

And it is also the sea, the sea, that surely underlines this. We regard the ocean as a kind of blank canvas. We pollute it unknowingly, because we cannot see the results of our abuse. But a cetacean, living in the water yet breathing the same air as us, is a stupendous and exquisite symbol of the life down below.

When a humpback whale breaches, as I've often seen it do, throwing its 50-ton, 50-foot body out of the water, it is an absolute physical rebuke, a literal breaching of the barrier between us and the element that covers two-thirds of the Earth. It is a renewed reminder that, in the 20th century alone, we hunted and killed more than 300,000 blue whales. Only 15,000, at most, remain.

But this is not just a tale of exotic and charismatic megafauna. As the British wildlife trusts point out, there are many cetaceans around our islands, susceptible to the same problems. Only last month a fin whale was carried into Portsmouth Harbour on the prow of a merchant ship. It had almost certainly been struck at sea by another ship. This whale – a species second only to the blue whale in size, the fastest of all great whales and also one of the loudest (a fin whale in the eastern Atlantic can hear a fellow fin whale's call from the other side of the ocean) Ω met an even more ignominious end, being carted off to landfill.

The Hampshire and Isle of Wight Wildlife Trust, with whom I work, is a great advocate, like the rest of its peer trusts, for the conservation of marine species. A couple of weeks ago it identified a small pod of porpoises playing off Sandown, on the Isle of Wight, within easy sight of land. One intrepid local naturalist, Captain Keith Leeves, has even instituted whale-watching trips in the Channel.

There is a heartening story here, too. We are much more attuned to the plight of the seas – partly through campaigns such as Hugh Fearnley-Whittingstall's. Cetaceans are also reaping the benefit of the international moratorium on the hunting of great whales. It celebrates its 30th anniversary this year, with an ambitious WhaleFest to be held in Brighton this October, complete with life-size inflatable whales to be installed in the Hilton's ballroom – the same hotel where the moratorium was signed.

We have come a long way in those 30 years. Yet we still know so little. Scientists such as Hal Whitehead have been doing amazing work on sperm whales – which possess the biggest brain of any animal that ever lived. Professor Whitehead has shown that these highly social animals have the ability for complex communication and even a culture of their own. American philosopher Thomas I White has pointed out the equally incredible private life of the dolphin, whose brain may be emotionally superior to ours, and capable of a sense of individual, existential self.

All this work is only in its infancy. What will we discover in years to come? Will we look back 100 years from now and wonder how we ever allowed these animals to be hunted, as they still are – by Japan, Norway, Iceland, the Faroe Islands?

At such moments I'm often reminded by a line from Douglas Adams' Hitchhiker's Guide to the Galaxy, when the Earth's dolphins escape its imminent destruction, with the throwaway line, "So long and thanks for all the fish".

Back in the 1960s, the radical scientist, John C Lilly, proposed that cetaceans were aliens with whom we merely shared our planet. Unfortunately, we may have altered the Earth's climate so much that those aliens feel increasingly under threat: from pollution, anthropogenic noise, and warming and acidifying seas that affect their food. It is ironic that 30 years after we thought we'd saved the whales, they may be in greater danger than ever before.

Organisations such as the wildlife trusts, campaigning for a vital implementation of 127 marine protected areas around our shores, and the Whale and Dolphin Conservation Society, for which I act as an ambassador, are the first line in the defence of cetaceans. But, as a writer, I look to art and literature as well as science and conservation to draw attention to their plight. Along with the artist Angela Cockayne, I have co-curated an ambitious attempt to create an online recording of Herman Melville's Moby-Dick, which launches next weekend at the Plymouth International Book Festival. Published in 1851, the book – widely seen as the greatest American novel – has never been surpassed as a commentary on the whale.

The intention of the Moby-Dick Big Read is to reimagine Melville's book for a digital, 21st century audience. The result, we hope, is a new awareness of the state of the whale. Melville's prescience addressed its possible extinction, even as he questioned the morality of the humans who pursued the whale. "I know him not, and never will", he wrote, after composing 136 chapters of his leviathanic text. How astounding that, 160 years later, we might still say the same thing.

For a map of the 127 marine conservation zones proposed by the wildlife trusts, go to: wildlifetrusts.org/MCZmap. For the Moby-Dick Big Read: plymouthinternationalbookfestival.com