Probing the emotional lives of animals is new territory for biologists. A couple of decades ago, emotions were off-limits: scientists studying animal behaviour focused on what they could see animals doing, not how they might be feeling. Yet questions of animal emotion underpin animal welfare – as Jeremy Bentham wrote in 1789, “The question is not, ‘can they reason?’ nor ‘can they talk?’ but ‘can they suffer?’” The growing animal rights movement forced us to consider animal emotion, and we now know a great deal about how the vertebrate brain generates and makes use of what we humans experience as “feelings”.

A whole other layer of complexity arises when thinking about the animals that share our homes, especially dogs. Most dog owners are convinced that their pets not only lead complex emotional lives, but also know what their owners are thinking. Study after study seems to provide support for these notions: most recently, scientists at the Messerli Institute in Vienna have shown that dogs can discriminate between human faces that are expressing different emotions, even when they can only see half the face, and the person in the photo is completely unfamiliar to them.

Unfortunately these studies, taken as a whole, provide little comfort for those who would like to believe that dogs are little different to humans, apart from an inability to talk. Not only is their emotional life distinctively different to our own, the evidence also suggests that the way they perceive us bears little resemblance to the way we think they do. Dogs probably only feel about half the emotions we do (but may, as a result, feel them more keenly). Emotions can be roughly divided into two kinds – basic emotions or “gut feelings”, which arrive without warning, and “reflective” emotions, which require conscious thought.

A cockapoo. Photograph: Alamy

Fear, affection and anxiety fall into the former group; guilt, pride and grief into the latter. All mammals examined so far have the brain structures that enable them to feel the same basic emotions that we do, and now that dogs have been trained to lie still in an MRI scanner, we can add them to the list. But what about more the complex emotions, those that don’t emerge in our own children until they are several years old?

Most dog owners believe that they can identify their dog’s “guilty look” when it’s done something wrong, but several studies have blown that myth apart. The “guilty look” is no more and no less than the dog’s anticipation of some kind of punishment, based on its interpretation of its surroundings and its owner’s body language. This was first suspected to be the case almost four decades ago, when a veterinarian advised a client whose dog was ripping up papers while he was out to place torn paper on the floor and leave the room – when he returned a few minutes later, the dog (which had not moved throughout) looked as “guilty” as if she had done the ripping herself. More recently, Alexandra Horowitz of Barnard College in New York was able to induce “guilty looks” in dogs simply by telling their owners that they’d done wrong – even when they hadn’t – and tellingly, the strength of that “guilty look” matched the severity of punishment that each owner normally used when the dog transgressed.

A Boston terrier plays in the snow in Nottingham. Photograph: Laurence Griffiths/Getty Images

However, at least scientists and owners concur that dogs do have emotional lives. More unpalatable may be the opinion of some scientists – now probably in the majority – that while dogs do love their owners, they don’t realise that their owners love them back. On balance, it’s difficult to avoid the conclusion that dogs don’t perceive their owners as thinking beings at all. Precisely which animals possess a “theory of mind” – the ability to attribute mental states to others – is hotly debated, as is the precise age at which human children first exhibit this skill.

Given how responsive our dogs are to us, it’s tempting to believe that they do understand us, and indeed dogs pass several theory of mind “tests” (imitation, deception, role-taking, responding to begging) – in some instances, more convincingly than chimpanzees do. Yet there are simpler explanations for all of these abilities, and so far no convincing evidence has been produced to confirm that dogs understand that we have minds, or have any comprehension of the relationships they have with their owners.

That’s not to say that dogs are mindless robots: far from it. The science of canine behaviour is revealing something potentially more exciting, that dogs have evolved their own mental toolkit for living alongside us, one that’s not the same as ours, but perhaps equally exquisite. They are astonishingly attentive to everything we do, they can probably “read” human body language better than we can, and they are incredibly fast and flexible learners. Having lived alongside us for thousands of years, they have evolved not only an inbuilt affection for mankind but also a set of skills for becoming our “best friends” – even though they have little understanding of how we feel about them.