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There is the river we know, and there is also another river.

This is something I came to understand when I was a boy, growing up among the sawmills and net lofts along the Lower Fraser River, and under the bridges and in the backstreets of Burnaby, which lies in the middle of Greater Vancouver, on Canada's west coast. It's something I've been thinking about quite a bit lately.

It comes up whenever I read the dispatches from the front lines of that necessary war against obscurantism and the lethal irrationality of God-belief, from the likes of Richard Dawkins and Christopher Hitchens. It also comes up when I read the philosophers Charles Taylor and Eliott Sober, and when I read the work of that great explorer in the science of evolutionary biology, E. O. Wilson.

More than a decade ago, Wilson wrote: "The choice between transcendentalism and empiricism will be the coming century's version of the struggle for men's souls." We are only a few years into that century, and you could say we are already kneedeep in that bloody struggle.

Still, the lower reaches of the Fraser River weave and thread their way through the cities and suburbs and remnant farmlands of Greater Vancouver. The waters move heavy and dark, emptying a mountainous and forbidding domain roughly the size of the island of Britain, and here the river still empties into the sea.

But this is the river we know. There is also another river.

Just as there are towns and villages along the river we know, there are towns and villages along the other river. Sometimes, when the light is strange, or when it rains and floods and the world is dangerous, or when you have undergone great privation, or fasting, you can see people in canoes, from the other river, out of the corner of your eye. And sometimes, those people can see you.

The name the old people have for the people of the other river is st'lalakum. And the name those people have for us is also st'lalakum.

I can't be certain that I have all this quite right. It helps that I occasionally made these matters the subject of my inquiries over the years as a journalist. But what I know of the old cartography of the world where I grew up was already embedded in my consciousness from the understanding I first acquired, when I was very young, from Sto:lo people, and Katzie people, and from Tsawwassen people.

These are the names of the tribes who have lived along the Lower Fraser and its tributary rivers and sloughs from time out of mind. These, and the Musqueam, the Kwantlen, the Semiahmoo, the Coquitlam and the Tseil-Waututh people. Wave after wave of smallpox and other infectious diseases decimated them, but their descendants are here yet, on the tiny reserves that enclose their old villages, around which the great cities of Canada's west coast have arisen. Some of those villages are thousands of years old.

Yet even now, the people will tell you about that other river, and they will do so even as they pursue careers in the sciences, or the arts, or drive buses, or persist in what's left of the commercial salmon fishery, and otherwise go about their lives, getting by, pretty much like everyone else.

The world is a palimpsest, and as soon as a story is told to make sense of things, it is a rare thing for it to vanish out of the world entirely. Once you hear these stories, you will never see the river we know in quite the same way, nor the cosmopolis that has grown up along its banks, and those stories will echo in everything you hear for as long as you may live.

The streets where I grew up are now gone. We were Irish Catholic immigrants, and the neighbourhood where we settled now lies buried beneath Metrotown, a vast complex of malls, office towers, banks, shopping centres and boutiques. It is the epicentre of a Euro-Asian metropolis of more than three million people, with extensive economic and cultural ties to Guangzhou and Shanghai and Hong Kong.

But even when I was a boy, in the streets above the Burnaby flats, where the Cantonese vegetable farms along the river went on and on forever, we knew that something had gone before all of us, too. The faint outline of older stories was on the ground. Down the railroad tracks, mountains of blackberry, salmonberry and morning glory engulfed the tumuli of long-shuttered factories and mills. Even the vast and long-dead Ford Assembly Plant on Kingsway was swallowed up in it, but its ruins were still there.

There was the Labour Temple at the top of my street, from the days when everyone sang the Red Flag, and the socialist orator Bill Pritchard was put in jail for seditious conspiracy, and so the people elected him mayor. There was a general strike, and the Army of the Common Good rose up from the ranks of the poor, and printed its own currency, called labour units. Everyone called them lulus.

The old men at the Jubilee pool hall told those stories, but underneath all that, just a block east of the Labour Temple, in 1969, Don McIntyre was doing some minor excavating in his basement and found what turned out to be a huge stone from an ancient circle of stones, which would have been 13 metres across in its day. It was a mystery. And on a fine spring day when I was fishing for oolichans with a Sto:lo friend, Ernie Crey, we came upon a small mystery of our own.

We were net-fishing from a canoe in a back channel of the Lower Fraser, behind a small island, McMillan Island, under the roaring traffic of the Port Mann Bridge. There, we came upon a row of stubby posts from what looked like an old pier, poking up out of the riverbank. We told an archeologist from the University of British Columbia about it. Later, she told us that indeed it was once a kind of pier, probably for fishing, and she'd had the stakes carbon-dated, and they were about 1,000 years old.

From the windows of my high school, I could see across the river to Burns Bog, a wild and barely-penetrable place of gloomy forest and miniature trees and carnivorous flowers and swamp, if you can imagine a thing like that wholly enclosed by one of the most heavily-urbanized landscapes in Canada. Above the bog was a great ridge, and the suburban neighbourhood called Sunbury. During the 1960s, when the winds blew heavy from downriver, bones would fall from old grave boxes placed high in the cedar trees, after the burial customs of the people from the centuries before.

Just upriver from the edge of Burns Bog, if you walk along the river at low tide, below the ruins of the Saint Mungo salmon cannery, there is another old pier, an assemblage of heavy cedar stakes sticking out of the mud. In the 1990s, some archeologists carbon-dated those and found them to be 4,500 years old. The pier is adjacent to a place that was once a village, and the bottom  layer is 9,000 years old. Burns Bog was a place that was notorious for its portals into the river of the st'lalakum.

Another such place, far up the Fraser Valley, is Cultus Lake. A long time ago, they say, a man once weighted himself with a stone, and sank to the bottom of the lake, and landed on the roof of a house of st'lalakum. It is also said that the bodies of people who drown in Cultus Lake are sometimes swept away in a kind of subterranean passage that roughly parallels the course of the Fraser River, and their bodies will be found more than 100 kilometres distant, on the seacoast, at Point Roberts.

There is another dangerous place, a morning's walk from the place where the Pitt River enters the Fraser River about 30 kilometres upstream from Vancouver, on a small tributary river called the Allouette. This is also a place where sometimes st'lalakum were seen. And here, too, they say a subterranean passage leads all the way to that same spot at Point Roberts.

It was at Point Roberts that X:als, the Great Transformer, came into the world. It was several thousand years ago, the old people say, that X:als arrived there, with two companions, and 12 servants, and he started his way upriver. On his journey, he separated people from animals, and changed the wicked into stones, and generally went about the work of bringing order into the world, setting down the laws, and so on. The story is like Beowulf, or the Ramayana.

At one of his last encounters in the realm of the river people, before he went up into the sky to become a star, X:als is said to have engaged in a great battle with some sort of shaman, about 120 kilometers upriver from the sea, at a place within the steep walls of the Fraser Canyon. The place is called Tatxlis, which means Gritting His Teeth. The shaman, whose name was Qewxtelemos, stood on the far bank of the river, and he and X:als battled with strange medicine powers and thunderbolts. There is a large stone at Tatxlis, and it is covered in deeply indented striations, like scratch marks, which were made, they say, when X:als worried his thumbs into the rock.

In the summer of 1808, the great explorer Simon Fraser, after a five-year journey from Montreal, was passing down through the canyon of the river that was to bear his name. He came upon many people and many stout villages, and he was brought to the Tatxlis stone, and its adjacent village, on the afternoon of June 28.

That evening, he recorded this in his diary: "At the bad rock (Lady Franklin Rock), a little distance above the village, where the rapids terminate, the natives informed us that white people like us came there from below; and they shewed us indented marks which the white people made upon the rocks, but which, by the bye, seemed to us to be natural marks."

What appears to have occurred here is that the Sto:lo people of the canyon mistook Fraser for a relation of X:als, the Transformer, and Fraser mistook his Sto:lo hosts to mean that white people made the marks in the stone. Fifty-years later, in the pages of the New Westminster Columbian newspaper, something else was slightly lost in translation, in this way:

June 27, 1863. "A Mermaid In The Gulf." Mr. Graham, who is erecting a saw mill on Burrard Inlet, has just given us an interesting description of one of those mythological marine mammals  which he saw on Monday week in the Gulf of Georgia, about midway between the Inlet and the mouth of the Fraser.

 It was about 6 o'clock p.m., when he saw it gradually rise above the surface of the water within about 30 yards of where he was, showing the entire bust, in which position it remained for the space of five minutes looking in the direction of the boat in which he and two Indians were sitting, when it slowly sank into its native element.

The Indians evinced considerable alarm at the strange phenomenon. Mr. Graham describes it as having the appearance of a female with long hair of a yellowish-brown tinge drooping over its shoulders, the color of the skin being a dark olive.

The Indians have a legend  that if this animal is seen and not killed, those by whom it is seen will pine away and die, and relate an instance of the kind as having occurred amongst the Squamish Indians at the sight of the one alluded to. They also state that many years ago one was killed on Squamish River by an aged Indian.

To my knowledge, this is the first instance of a white man – a man of the x'wilitem, the "hungry people," as people of the settler cultures are known in the Halkomelem language – reporting the sighting of a st'lalakum. And here, too, as in Simon Fraser's case, it was a matter of someone seeing something, and not seeing something, at the same time. There is the river we know, and there is also another river.

The story the Squamish boatmen told of the "mermaid" in the Squamish River is a classic st'lalakum story, and it just so happens that we may know the origins of the st'lalakum Mr. Graham saw, because she matches the description Mr. Graham' gave of his mermaid. That st'lalakum is intimately associated with a place on the river that is only a few canoe strokes from the 1,000-year-old pier remnants that my friend Ernie and I came upon while we were fishing oolichans.

At that place, there is a small river that empties into the Fraser called the Coquitlam, and the story about it goes like this.

In the weeks before X:als had his lightning-bolt battle with the shaman Qewxtelemos, at Tatxlis, and just a day or so after he turned some Kwantlen people into wolves at a place that is now at the right-bank abutments of the Patullo Bridge that carries rush hour traffic across the Fraser River at New Westminster, X:als turned a foolish man to stone, just upriver from the Coquitlam mouth.

This is the very spot near the Port Mann Bridge where Ernie and I were fishing. You can still see the stone man at low tide there. His name is "Deaf," because he took some while to respond to X:als, when X:als first called out to him. In the way the famous Katzie "Indian doctor" Old Pierre told this st'lalakum story to the ethnographer Diamond Jenness in 1936, X:als was quite busy at this place near the Coquitlam mouth.

It was here that X:als changed one man into a mink, another into a bear, another into a kingfisher, another into a sandhill crane, and yet another into a raccoon. He made one man disappear into the bottom of the river. He took a crying child and transformed it into a magic being that down through the years would sometimes appear to people, in whirlpools, and bring them great luck.

There was a haughty woman there who was made angry by all this commotion, and X:als condemned her to an eternity as a st'lalakum. She made her abode at the bottom of Coquitlam Lake, in the mountains, but sometimes she would move downstream, into the Fraser River, at night. When Old Pierre told Jenness the story, he said that about 80 years earlier – so, in the 1850s or 1860s – this st'lalakum was seen by a Coquitlam woman who had gone down to the river with a pitch wood torch, to draw water.

"She saw a wave coming up the stream, and behind it, a woman with long trailing hair," Old Pierre said. "The old woman hurried home and related what she had seen, and fell dead."

To return to the 21st century's great "struggle for men's souls," we now have to return back upriver to Gritting Its Teeth in order to appreciate something that makes E.O.Wilson's  necessary choice between "transcendentalism and empiricism" rather less straightforward than we might imagine. It involves seeing something, and not seeing something, at the same time. It is about the river we know, and the other river.

Almost everything about the people of Canada's west coast defies what Europeans, and indeed most North Americans, understand about "Indians." They were sedentary town-dwellers. They were stout and stocky, sometimes fully-bearded. In the Fraser Canyon, above Gritting Its Teeth, Fraser was admiring of the people's houses, "constructed like American frame houses." A few days later, he would pace off a grand cedar-framed longhouse, down in the valley, that he reported to be more than 400 metres in length.

It was also about the time that Fraser was coming out of the canyon that he came to realize that for five long years, he had been wrong. The entire purpose of his journey was to chart the great River of the West from the headwaters to the sea. It was only in the canyon, in the  days before his final descent to the sea, that he realized he'd been wrong, all along. This was not the Columbia River. This was another river, and it was now turning west, towards the seacoast, several degrees of latitude north of where the Columbia mouth was known to be.

At Gritting Its Teeth, I once sat with the Sto:lo tribal historian Sonny McHalsie, at exactly the same place that Simon Fraser was brought in 1808, at the very stone where X:als is said to have worried his thumbprints into the very rock. Generations of archeologists have come to this place. They have scoured and mapped and assiduously examined this place, and they had noted the precise location of almost every fire-cracked rock, every hearth, every ancient post hole, and assigned protected-site archeological registration numbers to each of them.

But there is something all those archeologists never saw, even though it was right there, in plain view, a mere 100 metres or so from the Gritting Its Teeth Rock, on the far side of the river, at a place called Xelhalh. It is the remnant of a massive stone wall, and what's still left standing is a section about 20 metres in length and more than six metres in height.

It is like something from the ancient fort of Dun Aengus, on Inishmore Island, in the Aran Islands, off Ireland's Galway coast. There are other walls just upriver of Xelhalh, only much bigger. They were built as defensive fortifications against the depredations of those Vikings of Canada's west coast, the dreaded Euclataws.

But all these fortifications remained unknown to the traditions of empiricism, until only very recently. Science did not see these things, and they were unrecorded, unprotected, and unseen, because archeologists have been trained not to see such things on North America's northwest coast. "Indians" were not supposed to build such things in these forests, on these rivers.

This is not to make the case for some kind of equivalence between the phenomena one encounters in the traditions of transcendentalism, and the stuff of the real world, as revealed by empirical method. I am not arguing for a "belief" in st'lalakum, or in forest giants, or cannibal ogresses.

But when I was a boy, I did not believe in the strange river monster that old fishermen used to tell me frightening stories about. Only later did I come to know the thing was real. When I became a man, I caught one. It was much bigger than I was. I let it go. The largest of these creatures on record was caught in the Fraser River near New Westminster, in the 1860s. It was weighed at 1,387 pounds. It was a Fraser River white sturgeon, Acipenser transmontanus, the largest freshwater fish in North America, the creature the Katzie people say is descended from the daughter of a great chief, Clothed With Power, who came down from the sky at the beginning of the world.

I also believe in the existence of The Trembling Giant, which lives near Fish Lake, at the edge of the Great Colorado Plateau, in Utah. It is an organism that weighs roughly 6,000 tonnes, takes up more than 40 hectares of space, and is believed to be several thousand years old. It is not as though this spectacular thing has been unseen by x'wilitem, or unknown to science. All sorts of people had been looking at it for years, but until 1992, everyone thought it was a forest. It turns out that it's a single organism, connected by a single, elaborate root system, and all its trees are genetically identical.

There is another creature, the two-headed lightning serpent, which shows up in the stories and the totemic art of almost all the people whose ancient homelands lie within sight of Mount Baker, the semi-dormant volcano just south of the U.S.- Canada border, in the Cascade Mountains of Washington State. The creature usually appears as a giant snake with the heads of Mallard ducks at each end, and it is said to be able to cause the ground to shake, and it makes horribly loud noises, emits lightning, makes you go crazy, and then flies away.

I believe quite firmly in the meaning of this creature, and its attributes. Ruth Ludwin convinced me. She's a research scientist with the Pacific Northwest Seismograph Network at the University of Washington.

As part of Ruth's inquiries into the volatility of the Cascadia subduction zone, a plate-boundary fault that lies about 50 sea miles off Canada's west coast, it came to her attention that there was something peculiar about the site of a long-ago encounter with one of these frightening animals, which occurred near what is now the Fauntleroy ferry dock, in Seattle.

Turns out the site sits right on top of a "a multi-stranded striking reverse fault" that runs beneath the waters of Puget Sound, through downtown Seattle, and across Lake Washington. The fault ruptured about 1,100 years ago, causing a massive tidal wave. Looking for more stories of encounters with this scary bird-snake – known to such local tribes as the Duwamish as the a'yahos – Ruth was directed to a place near the Seattle suburb of Burien, which proved to be the site of an ancient landslide. By pinpointing other a'yahos sites, Ruth managed to trace the entire east-west trajectory of the Seattle Fault.

In this way, the ancient geological history of the land itself is encoded in stories about the land, just as God-belief is encoded in our biology, and the human brain is patterned for storytelling, and the religious virtues, as they are known – compassion, forgiveness, altruism – are functions of the survival traits encoded in our genes.

But one has to be very, very cautious about these things.

That man who long ago sank himself to the bottom of Cultus Lake and exchanged songs and stories with the st'lalakum down there first had to undergo the most severe sort of "Indian doctor" training in order survive the experience. Ruth Ludwin at the University of Washington had to study the hard sciences for more than a decade before she felt competent to discern meaning in stories about the lightning-snake a'yahos.

The old woman who went to draw water at night and saw the st'lalakum woman walking along the bottom of the river fell dead after the experience. Those Squamish boatmen with Mr.Graham warned that if one does not kill the st'lalakum one sees, one may pine away and die. At the very least, as E.O. Wilson put it: "Those who hunger for both religious and intellectual truth will never acquire both in full measure."

They say the power necessary to survive encounters with st'lalakum can be acquired only through the Smitla secret-society rituals associated with the "longhouse religion," which was banned in Canada between 1884 and 1951. Since its revival in the early 1960s, among the Sto:lo, the Musqueam, the Katzie and the other Coast Salish peoples who live in the shadow of the gleaming towers of Vancouver, Seattle, and Victoria, more than a dozen people have died during Smitla initiations.

This is serious business.

During his descent through the darkest and most daunting sections of the Fraser Canyon, Simon Fraser wrote: "I have been for a long period among the Rocky Mountains, but have never seen anything equal to this country, for I cannot find words to describe our situation at times. We had to pass where no human being should venture, yet in those places there is a regular footpath impressed, or rather indented, by frequent travelling, upon the very rocks."

That is the river we know, now. It is not the river Simon Fraser thought it was, then.

Then there is the other river: "The map of the material world,including mental activity," writes E.O. Wilson, "can be thought a sprinkling of charted terrain separated by blank expanses that are of unknown extent, yet accessible to coherent interdisciplinary research."

These inquiries must go on. These dark and heavy waters all empty into the same sea.

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Victoria, July 21, 2008. Terry Glavin is the author of Waiting for the Macaws.