After years of experience in the laboratory, my relationship with the scientific method has become rather cosy. But brushes with those not trained in the ways of hypothesis and experimentation frequently give me momentary pause: friends who swear by untested dietary supplements, advertisements about the miraculous properties of shampoo or, in this case, a recently aired opinion about scientists studying animal emotions.

This opinion appeared in a letter to The Guardian. "So someone has done lots of scientific research and spotted that cows and sheep are not just unfeeling machines," the irate reader wrote. "The wilful stupidity of clever people beggars belief. What did humans evolve from? Asteroids? Old car batteries? Surprise, surprise, they evolved from animals. … So where did our intelligence and emotional behaviour evolve from? From our animal forebears? Never! Only overweening self-interest and wilful stupidity can have masked this from our culture for so long."

If you can navigate through the sarcasm, you may spot two technical problems with this reader’s position. The first concerns the nature of scientific procedure; the second the biology in question.

First let’s deal with the issue of ‘wilful stupidity’. The reader appears to be offended that scientists refuse to assume something is true, even if it seems rather obvious. Instead, they prefer to prove it.

Unfortunately, as trained scientists know all too well, things that are ‘obvious’ are not necessarily true. Indeed, the history of science can be fairly said to be the demolition of obvious truths by rational scrutiny and experimentation: that the earth is flat; that the sun rotates around the world; that illness is caused by damp air or witches.

Biology especially is notorious for not being obvious, for coming up with the most convoluted solutions to seemingly straightforward problems. Organisms have evolved in a hodge-podge fashion, not always as an intelligent overseer would have designed it. To flick on a genetic switch, biology sometimes doesn’t invent a simple ‘on’ switch, but instead makes an inhibitor switch that a further molecular switch has to switch off. Sort of the equivalent of someone saying ‘I’m not unhappy’; it’s cumbersome, but effective. And it gets worse: biology, not content with being merely cumbersome, has often evolved systems bordering on the monstrous – the linguistic equivalent of ‘I’m never not the opposite of not not not unhappy’. In this face of this confusing complexity, assumptions are ill-advised.

But let’s return to the reader’s beef – no pun intended. Is it obvious that cows have emotions? It is true that, as fellow mammals, we share a lot of common elements, but differences between us are also significant. Certainly, without seeing the data, I wouldn’t bet so much as steak-frites dinner on the presence or absence of complex feeling in cows.

And here is why: evolution is not always obvious, either. Moreover, you only need listen to the commonly heard argument ‘If humans evolved from apes, then why are the apes still here?’ to appreciate how little understood this branch of science is by the general public. It is absolutely crucial to remember that all current forms of life on earth evolved from simpler animals that no longer exist, animals sharing some but not all characteristics of the species that evolved from them. While we certainly did not evolve from car batteries, we did not evolve from cows either. We and cows evolved from a common ancestor that did not resemble today’s cows or humans but instead, something simpler and in-between. This intermediate ancestor – let’s call it, for the sake of argument, the ‘Cowman’ – lived about 80 million years ago and was probably as large as a modern guinea pig and about as smart. But we know nothing about its emotional capabilities.

A good scientist would reason this way: there are at least four possibilities about the emotional state of modern cows and the extinct Cowman, all of them viable options. The first possibility is the scenario favoured by the reader: that Cowman indeed had complex emotions and this trait was preserved in both branches when the lineage split. The result? Humans and cows both have basic emotions, albeit to varying degrees.

But there are other scenarios. The second possibility is that Cowman did not have emotions, and it was not until after the split in lineage that humans evolved advanced emotional capability and cows did not. There is a clear precedence for this sort of outcome; for example, humans evolved complex spoken language and cows did not. And before you start feeling superior, it’s important to stress that these sorts of recent tricks don’t all belong to us clever humans. Cows, in turn, evolved amazingly complicated ways of digesting grass, involving multiple stomachs, while we did not. In the world of digestion, we humans are rubbish. Indeed, a Gary Larson-inspired cow-scientist might look at our pathetic species disdainfully and decide to check whether we had digestive systems at all.

A third possibility is that Cowman did not have emotions, but this trait evolved independently in both the human and bovine branches after the split in lineage. We see this sort of effect all the time. For example, if you travel through the desert, you will notice lots of plants that look like cacti. But on closer inspection, many these are largely unrelated, as distant from one another as cows and humans. But it just so happens that cactus-like traits are the most optimal for harsh, arid conditions, favouring the storage and protection of water, so there is a strong natural selection pressure to evolve these sorts of strategies. Other traits are just so incredibly useful that they have evolved independently regardless of the environment: the wings of insects, bats and birds are a great example.

A forth possibility is that Cowman was an emotional beast, but as the cow lineage developed, emotions proved not to be terribly useful and the trait was eventually lost; in contrast, humans found emotions important for maintaining advanced social behaviour and kept it up. Useless things get lost during evolution all the time; humans lost their tails when they came down from the trees, whereas monkeys kept them; all we have to show for it now is a stunted tailbone at the end of our spine.

And when it comes to brains, the situation becomes even more uncertain. After the first proto-humans appeared, their brains changed at a staggering rate, both in size and complexity, even as other more basic functions, like the circulatory system, remained relatively unchanged. Because of this drastic alteration in the human brain, scientists who are interested in the evolution of emotions really need to have proof before they can declare a non-human species truly emotional. This is not out of ignorance, wilfulness, stupidity or ‘overweening self-interest’, but just because that’s the proper way of doing things. Next, having found some evidence that cows are indeed emotional, scientists now have more work to do to find out how it all works, and how such a capability evolved.

I do not blame the reader for her scientific ignorance, which I trust was not ‘wilful’. I can only assume that she, like so many other people, failed to receive adequate classroom training in the basics of evolution, or about the fundamental processes of the scientific method. Her assumption – that our evolutionary relatedness to animals suggests that joint emotions are likely – was in fact a reasonable starting hypothesis. I do, however, fault her for vilifying the well-meaning scientists who have devoted their lives to understanding these unknowns. Such studies may seem arcane and pointless to her, but – aside from revealing interesting biological facts – they may also one day lead to cures for emotion-linked diseases such as depression.

And insofar that much of this research is motivated by concern for the welfare of domesticated animals, they may even be good for the cows.