Take a good look around.

Look out of the window and under the floorboards and behind the furniture. Look up at the trees, and down the streets and in the lanes and alleys. Can you see it? The life that shares our towns and cities. The rats and the mice; the magpies, the pigeons and the gulls; the slugs, the spiders, the starlings and the squirrels. Will you call up the pest controller? Will you put up the nets or put down the traps?

Or will you come on a walk instead? A walk round the city with Esther Woolfson. She's the writer who changed our minds about rooks and crows when her memoir Corvus was published in 2009 and now her new book, Field Notes From A Hidden City, is going to change our minds about other species, specifically those that have moved into the cities and made their home among the glass and the concrete. Woolfson believes most of our attitudes towards these animals come from prejudice, misconceptions and bad science, and she wants to change that. She wants us to look at these urban animals anew. She wants us to meet the neighbours, and the first of them is the gull.

GULLS

At the edge of Aberdeen harbour, Esther Woolfson leans down to greet a new arrival. "Aren't you beautiful?" she says. And he is. A plump herring gull with an overcoat of brown, little black jewels for eyes and a demanding way of putting his head forward when he realises I have some bread to hand out. Above him, his relatives are circling; they dive and rise and dive again before lining up on the harbour wall as if they've been taught how to queue politely. Woolfson is enchanted by it, hypnotised.

Nearby, however, some Aberdonians – the type that come down to the harbour to stare at the sea from their cars – clearly don't feel the same way. They're glaring at us through their windscreens like we're mad, or even bad, for feeding the gulls, for encouraging them. And who can blame these humans – they're just displaying the typical behaviour of their species. Last summer, for example, The Herald was full of letters from readers in the west end of Glasgow complaining about the "cacophonous squawks" that were keeping them awake. And raise the subject of gulls with virtually anyone and within seconds you'll be told that they attack people (even though it's impossible to find anyone who actually has been attacked); you'll also hear a long list of accusations against the species read out like charges in a courtroom.

It's an attitude that enrages Woolfson. "Cacophonous squawks"? Not at all. She describes the call of the gull as a kind of wild music, and tells me about the astonishing inner life of the species. They're monogamous, capable of recognising each other and of respecting their neighbours. They also return to the same nests every year, with mated pairs who have spent the winter apart reuniting for breeding and recognising their partner from a distance on his or her return. They're remarkable birds and it's us – humans – who've reduced them to scavengers of kebab remains on Friday nights.

Woolfson says all we need is more knowledge. "I hope if we knew more about the gull's lifestyle, we would care more about them," she says. "It's all very well having television programmes about the Serengeti but when people know more about what happens in the Serengeti than on their own roof, it's sad."

She says most of the anti-gull feeling is down to misplaced fears about hygiene; it's a fear of bird dirt, she says, and there are worse things than bird dirt. She knows this because she has lived with birds most of her life. As described in her first book Corvus, a succession of them have lived in her house in Aberdeen, most famously a rook called Chicken, who's now 25 years old. There have also been magpies and parrots but at the moment it's just Chicken and a crow called Ziki, both of whom she rescued as fledglings.

We stand for a few minutes and watch the gulls. All the bread is gone but they're still hovering above us in case there's more. "People are amazed when I tell them herring seagulls are on the list of endangered species," says Woolfson.

The number of herring gulls has halved over the past 40 years as the birds have migrated from coast and cliff to city, and she imagines a future without them. Teachers will have to show their pupils pictures of gulls, she says, because there will be none left to look at in the wild. "How will future generations learn about the value of the life around them?" she says. "How will they know what they've lost?"

SQUIRRELS

We start walking away from the harbour past the fishermen's cottages of Footdee. On the roof of a little hut nearby, a chorus line of starlings is performing. When she was a young girl in Glasgow, Woolfson had a pet starling called Max and she remembers the exquisite sweetness of his evening solos. That said, she's wary of anthropomorphising animals. The result of that approach, she says, is to make some animals sympathetic and some not, which in turn gives humans a licence to discriminate between animals. We can't look at the natural world, says Woolfson, without imposing morality on it.

You can see this no more clearly, she says, than with squirrels. She tells me about the day she stood and watched a red squirrel and realised something important about it: the red squirrel doesn't change but our perception of it does. It used to be seen as a pest; now it is seen as a national treasure. It used to be hunted; now it is protected. In Field Notes From A Hidden City, Woolfson relates how the Highland Squirrel Club was established in 1903 and killed 82,000 reds over 30 years. "It was astonishing to find out how many red squirrels they killed," she says. "I thought: the red squirrels weren't so beautiful then, were they?"

But Woolfson finds the modern approach towards reds just as disturbing. Now, red is good and grey is bad; what's more, the grey must be wiped out because it is, in the pejorative vocabulary of the grey-haters, non-native. But what, asks Woolfson, does non-native mean? For a start, the length of the red squirrel's stay in Scotland is far from certain; there is no record of it before the 15th century. And even if we could establish its presence before then, how far back do we have to go to prove a species' native status? To which year would we return, asks Woolfson; to which golden age or stage of the life of earth? Which window of past perfection might we attempt to restore?

What Woolfson finds even more disturbing than this native and non-native debate is where it has led – in particular the genocidal, anti-grey mania it has inspired in some people. "There's a lot of funding in this area," says Woolfson, "and there's almost a political agenda behind it, a nationalistic agenda. I saw one website which talked about diseased foreigners coming up from England. It's the same language that racist groups might use. Do we need a national animal to prove something? I'm very uneasy with some of the ideas that stirs up."

Woolfson's preferred strategy is non-intervention, and she's speaking as a reformed interventionist. There was a time when she couldn't stop rescuing birds and then, with more knowledge, she realised that a bird on the ground is just as likely to be learning to fly as it is to be abandoned. The same applies to red squirrels, she believes. Species change, they fall and rise, some become extinct. When humans interfere, they get it wrong and make things worse. So stop interfering, she says. Mind your own business. Butt out.

RATS

We're walking past the harbour now and the streets of warehouses that face it. One of them is called Baltic Place, which, as Woolfson says, is a street name, not a description. This is where the rats live. Everywhere is where the rats live. But Woolfson wants you to think again about rats too, although, as we'll discover, her relationship with this species is a little more nuanced. The problem for rats, she says, is similar to the problem for grey squirrels – they are subject to all kinds of cultural, mythological and psychological assumptions, some of which are wrong. The Black Death, for example. Everyone blames the rat for spreading it but Woolfson's book includes research by the archaeologist Barney Sloane which suggests the transmission of the plague was from human to human and not from rats at all. Rats are also adaptable, clean to the point of obsession, and intelligent with complex social behaviour.

And yet, when Woolfson discovered rats had moved into the space under her house in the city's west end, she called in the pest controller. How could she do it – after all she's said, after all the pet rats she and her family have lived with?

She says she did it because she has an obligation to her neighbours and to society. "I hate it but what can you do? Nothing else works and they breed very fast. You do have a responsibility when they turn up not to encourage them. It wasn't something I did without thinking about it."

And it doesn't stop her being horrified by what we continue to do to rats, the way vivisectionists use them. She once adopted a former lab rat, a young albino with a torn ear where the lab tag had been ripped out, and she describes how she had to help him groom and wash. He seemed, she said, a diminished creature; he seemed to have lost his essential rat-ness. She also describes how a scientist came to visit her once and went to the back room where she kept her pet rats. At the end of an evening handling them and watching them closely, he asked an important question. "I wonder," he said, "if it's really necessary to experiment on rats."

SLUGS

Now there's a word for you: slugs. Is there any English word less gracious, Woolfson asks, any word more co-opted as an insult, containing as it does most of the letters of the word "ugly". And yet slugs are good. They eat things and are eaten by things; they break down organic matter. In one extraordinary section of Field Notes From A Hidden City, Woolfson describes how a man used the mould-eating species of slug to remove all the rotten grout in his bathroom.

So why is the slug still the poor relation of the snail? Is it because the snail has the decency to cover up with a shell? Is it because the slug flaunts its nakedness? Is there a prudishness in us that can't stand the ostentatious, mucusy love-making of limax maximus, which mates at the end of a long string of self-created slime?

But even here, Woolfson uncovers some extraordinary facts. Slugs reuse their slime trails, travelling on their own pre-slimed routes, rather like rail commuters. By following these trails, they find their way back to where they came from, demonstrating, says Woolfson, that impulse that stirs in so many of us, the impulse to return to the place we regard as home.

Largely because of knowing these things, Woolfson is horrified by the appalling war we wage on slugs. She tells me about one gardener who recommended driving pins through slugs to kill them slowly and quotes the philosopher John Locke on the kind of humans who kill animals: "The killing of beasts will, by degrees, harden their minds towards men - people should be accustomed, from their cradles, to be tender to all sensible creatures."

"The more I think about it," says Woolfson, "the more I think that quotation from Locke is important, whether we're talking about rats or squirrels or putting pins through slugs. It does no good to human beings to behave like that. It hardens us."

SPIDERS

We've jumped in the car and headed up to Old Aberdeen. As we get out, a rook in the tree above starts calling out raucously, joyously. We look up as he stands at the end of a branch and shouts. Why on earth do people fear these birds, asks Woolfson. What on earth have they ever done to us? She thinks movies may have a lot to do with it – the old horror images – and the idea of the corvid picking at dead bodies. People are remarkably superstitious and morbid, she says, and the old mythology, the old fears, have a habit of lingering; they never go away.

The same applies to spiders, she says – even more so, in fact – although in Field Notes From A Hidden City Woolfson celebrates the very qualities and strange attributes that some people find frightening: she documents the strangeness, the ways they are different from us, the lungs that look like the pages of a book, their exoskeleton, the web-making spinnerets.

As with slugs, she also lists the ways in which spiders are useful. "They are pest controllers and important food in their turn for birds, bats and small mammals," she says. "We lose spiders at our peril." They are also a useful way to judge people's character and values. "I find it strange when people say they don't like spiders," says Woolfson. "In fact, I judge people by their attitude to the natural world in general." She quotes the poet Patrick Lane: "I measure friendship by those are the friends of spiders and those who are not."

We're back in the centre of the city on Union Street. There's a busy crossroads here, near Union Terrace Gardens, the park the council controversially wanted to tarmac over until the idea was thrown out. Crowds of starlings used to put on a nightly show here. Esther Woolfson remembers it. The sky would be scattered with dark ingatherings of darting commuters, she says, in a sweep and flight that transformed the sky, the city and the lives of the observers. And then officials put nets up on the bridge where the starlings roosted and the crowds of starlings had to move on. Are they still out there somewhere, wonders Woolfson. She talks about Edwin Morgan's poem The Starlings In George Square and its terrible, jabbing question: "Do we deserve the starlings?"

Woolfson asks if this is the way it's always going to be, until the end. Are we doomed to run Genesis backwards, to un-create? Perhaps the recent controversy over foxes, and Boris Johnson's call for a cull, is an example of it, although Woolfson doesn't tackle the issue of foxes in her book as they are so scarce in Aberdeen. She thinks the only source of hope is to un-hate, to learn new ways of thinking about the animals that live in the city with us. "We despise the creatures that choose to live in the city and I don't know why – is it an expression of dissatisfaction with ourselves?" We should learn to celebrate them, she says, and maybe that way we will learn how to save them too.

Field Notes From A Hidden City: An Urban Nature Diary by Esther Woolfson is published by Granta, priced £16.99.