THIS spring and summer, two pairs of birds have chosen to nest near one of my windows, within easy binocular-gaze, one in the beech tree across the road, the other on the chimney of the building behind it.

To be able to observe the processes of nesting in the centre of a city has felt like a privilege, an invitation to cross, however briefly, a bridge between two worlds.

The species involved are Pica pica and Larus argentatus – magpie and herring gull – and the knowledge that both are despised, as are most creatures found within cities, has made me think about our strange attitude to urban nature. Hostile to the wildlife in our midst, we view with equanimity the destruction of the natural aspects of our own metropolitan surroundings, accepting that there must be more roads to accommodate more cars, or that constructing more "retail space" will enhance the quality of our lives.

These attitudes are indicative of a mindset that views cities as lesser places, ones already so far contaminated by modern life that our moral, spiritual and mental wellbeing must lie elsewhere, in countryside, empty places, in elemental "wilderness".

Many of us maintain the illusion that our state of being urban is temporary and that out there, somewhere, is the place to which we will "escape".

The same activities carried out in cities are not regarded as of similar worth – a countryside walk is deemed superior to a city one, although involving the same expenditure of time and effort. (In Scotland, the view seems to be that a hefty degree of discomfort enhances the moral value of any activity.) The danger is, while we idealise the non-urban and our own imagined place in it, we feel less inclination to defend and protect the environments in which, increasingly, most of humanity has to live.

If we regard distant places as more desirable, the same is true of animals and birds. Our attitudes to the natural world have been shaped over centuries by the influence of Aristotle's scala naturae or "great chain of being", which saw all nature as hierarchical: humans poised just below God and angels, with everyone else arranged in the descending order of value which encouraged the anthropocentric, self-serving view which has dominated our behaviour towards the rest of the living world. We approve selected animals as "iconic" or "charismatic", for reasons that are often questionable. Accustomed to viewing the natural world through a screen, we accept the premises of television wildlife programmes which encourage evaluation of other species in terms of human attributes: courage, victimhood or nobility. Feeling that the best is where we are not and that the rare or exotic are of more value than the local, we travel to see species considered of interest, involving the very planes or cars which increasingly cause the degradation of the habitats in which these creatures live.

If we view cities as places of lesser worth, we hold the creatures who inhabit them in no higher regard. We maintain a kind of apartheid of species – those we choose to nurture and those we despise and wish to destroy, dividing urban creatures, according to the environmental architect Fritz Haeg, into "pests or pets" according to a set of obscure, often sentimental, always unscientific values.

The animals we approve of are in the main dogs and cats. Keeping pets allows humans to have a relationship with "nature" while keeping a suitable distance from the realities of the natural world. With pets, we are allowed to be the kind of people we like to think ourselves to be while behaving towards the rest of the natural world with impunity.

Wild creatures and birds are subject to particularly harsh judgments, most being described as "vermin" and condemned for being populous or dirty (both areas in which we ourselves excel) even when they are not. Crows, raptors, gulls, rats, starlings, spiders, pigeons and foxes are all regarded as intruders upon our space. "Songbirds" are encouraged although magpies (themselves of the sub-order Corvida and therefore songbirds) are not. Grey squirrels are to be discouraged or, as they have been in Aberdeen, systematically killed to facilitate an increase in red squirrel populations. The romanticism surrounding the red squirrel illustrates, if nothing else, the fickleness of fashion. In the early 20th century, 82,000 red squirrels – regarded as forest pests – were slaughtered by the Highland Squirrel Club.

Urban species are not given the same ethical considerations which we give to the animals we eat, experiment on or whose living conditions concern us. In a recent radio comedy show, an audience was reduced to howls of laughter by the proposition that "we should kill a pigeon every day". The use of shovels was suggested. In the days when non-humans were considered insensate, lacking feeling or intelligence, it might have been acceptable to act callously towards them but with our knowledge of the vital interdependence of species, there are no excuses.

We seem not to ask why a robin or blackbird might have more right to feed and live than a hawk, or the domestic cat which kills more birds for sport throughout the year than the magpie which eats fledglings seasonally, to live. Contrary to common prejudice, magpies do not reduce garden bird populations. It may be unpleasant to watch a magpie attacking a blackbird's nest, but blackbirds produce more young than they need to reproduce numerically and this is part of the natural world in which we should not interfere.

Human sensibilities seem to play little part as colonies of other species are removed and destroyed. Gardens are covered by paving, turning them into sealed mini-car parks which destroy habitats and greatly increase the risk of urban flooding. Even more frequently, municipal authorities justify their brand of depredation, such as the removal of starlings, by invoking spurious notions of "hygiene". Bird excrement is supposed to "carry diseases" but does only to the extent – and often much less – than does the excrement of other species. (People walk around carrying bags of dog mess, our streets are littered with black plastic bags full of it but, all of a sudden, we're concerned about hygiene?)

What do we really know about the creatures we despise? Might they be intelligent, aware, social, monogamous? Might they be capable of concepts we believed related only to ourselves – high cognitive function, episodic memory, theory of mind, consciousness? The crow family has been designated by those who study them, "flying primates". Magpies are one of the three species on Earth able to recognise themselves in mirrors. (The others are higher primates and us.) Abilities such as problem-solving and memory exist in spiders, slugs, snails and worms. Many species display "site fidelity" – in other words, they are attached to their homes, as we are. Some engage in co-operative behaviour such as care for their community's young or sick and many, such as rats and magpies, have been shown to feel love, grief and empathy. Once we thought we knew all about pigeon navigation. Now we know we don't and that our understanding of its mechanisms lie in the field of quantum physics. What don't we yet know? If we knew more, might we care more?

Does any of this matter? Is it important that there are other life forms and presences within our cities? Does it matter if there are places where we can walk freely in fresh air?

The fundamental answer must be that to live thoughtfully, environmentally as well as in other ways, is better than available alternatives. Life on Earth in all its forms is increasingly fragile in the face of changes we struggle to comprehend or control. If we're protective of the lives of other species, we enhance our own. If we preserve species and habitats, we do so for our sakes as much as theirs.

If we appear passively to accept the destruction of trees or grass or gardens, we fail to realise that when the species inhabiting these places are lost, their loss diminishes us all. The recently published State Of Nature report tells of the drastic declines of urban wildlife: 60% of the 658 species for which there is data have declined, largely due to human activity through pesticides, building policy, removal of habitats, the atmospheric pollution and the wanton overuse of cars which turns our cities into places of fumes, noise and danger.

In his 2005 book Last Child In The Woods, a study of children's alienation from nature, Richard Louv coined the term, "nature deficit disorder" and while the suggestion of medicalisation might be questionable, the underlying truth is inescapable: for many reasons, including our fears of other people and traffic, children have few opportunities to immerse themselves in the natural world; to roam, to be alone to observe, listen, watch and delight in what's around them. As a result, we may be handing the future to generations who, unaware of what there is to be lost, may not know how to save it. (With perverse circularity, we safeguard our children from the dangers of large vehicles by endangering other people's children by driving them ourselves.)

It's not nostalgic, Luddite or reactionary to fight against the continuing depredations wrought upon our cities by developers, cars and the thoughtless destruction of natural places. The importance of green space has been underlined recently by the explosion of anti-government demonstrations in Turkey, sparked by the threatened destruction of a park (although it may be a vain hope that this will discourage the rapacious rich from viewing every park or garden as an economic opportunity).

Such concerns are all too real for those of us who live in Aberdeen since the lovely sunken gardens in Union Terrace, part of the Victorian system of bridges and viaducts, with its mature elms and long-standing colony of nesting rooks, narrowly avoided being destroyed and replaced with an anachronistic, glorified shopping mall of breathtakingly banal and vulgar design, instigated by people who have no need of public gardens in which to picnic on warm days. (The processes underlying this sorry project were as venal, skewed and undemocratic as to make a chamberful of Ukrainian politicians blush and left many of us with a sense of both environmental and political anxiety about future developments in Scotland.)

The need to defend and enhance urban nature is worldwide. In the interests of the vast majority of the world's population – the urban population – it's urgent to think newly about the future of cities and how we live in them and with whom, for one day, we may not even be able to dream of having somewhere else to go. Innovations and concepts in urban living such as "re-wilding" and "re-naturalising", ideas of "vertical farming" and "re-enchantment", of eco-cities where sustainability does not hinder progress, are all attempts to make the cities where we live ones in which we're content to be. We have to think differently and radically. If pigeon populations require control, why not follow examples from the Netherlands and set up municipal pigeon lofts? Why not use fewer pesticides in our gardens and encourage the wildlife around us? Why not use to the full unused green places in our cities, drive less, observe more? If we did, there might be less inclination to "escape". There's nowhere that wouldn't benefit from radical thinking; Scottish cities, lovely as they may be, need to optimise green space, not least, for the sake of residents without gardens.

In the meantime, I go back to the view through binocular lenses, to the stately Lars argentatus gazing down upon a frenetic world from the calm of its rooftop nest, to its long-legged chicks who soon will totter uncertainly amid the traffic of Aberdeen, to the shadow behind the leaves which is the nest of magpies where, inside a complex construction of twigs, some of the most beautiful, dazzlingly intelligent of nature's creatures are preparing to take their place among us.

Esther Woolfson's first book is Corvus: A Life With Birds. Her new book, Field Notes From A Hidden City (Granta, £16.99), charts one year observing the natural world of her home city of Aberdeen. She appears at the Littoral strand of the East Neuk Festival on July 6 and 7