There is a story about human evolution that has been repeated so often that it has stopped sounding like an argument and started sounding like a fact. Our ancestors mastered fire and began cooking. Cooked food was easier to digest and yielded more usable energy. That extra energy helped support larger brains. As food became softer and easier to process, enormous jaws, powerful chewing muscles and large digestive systems became less necessary. Over a million or two years, the ape became the cook and the cook became us.

It is a wonderfully neat story. Perhaps too neat.

Start with what is not particularly controversial. Cooking really does transform food. Heat gelatinises starch, denatures proteins, softens plant material and connective tissue, and kills many pathogens. In an important sense, cooking performs part of digestion outside the body. Richard Wrangham famously developed this idea in his "cooking hypothesis": fire did not merely give our ancestors warmth and protection; it may have fundamentally changed human biology by changing the energetic economics of eating.

Modern humans certainly look like animals accustomed to processed food. Compared with other primates, we have relatively small teeth and jaws and much less formidable chewing equipment. Our digestive system is also unusual for a primate, while our enormous brain is metabolically expensive. The adult human brain accounts for roughly a fifth of resting energy expenditure despite representing only a small fraction of body mass.

Put those facts together and the inference is attractive. Our ancestors effectively moved part of their digestive system outside their bodies and into the fire. Less energy and anatomical machinery were required to process food, while more energy became available to support the brain.

So far, so good. But there is a problem hidden inside this elegant story.

Cooking is a behaviour. Smaller jaws, altered digestive anatomy and larger brains are inherited biological characteristics. Learning to roast meat does not rewrite the genes in your sperm or eggs. A lifetime of eating soup will not cause your children to be born with smaller teeth.

For the biological changes to occur, natural selection still needs heritable variation upon which to act. Once cooking changes the environment, people whose inherited characteristics happen to work particularly well with that new environment may leave more descendants. Over many generations, those characteristics can become more common.

That is perfectly orthodox Darwinism. But notice what has happened to the simple story. Cooking does not produce the biological changes. It changes the circumstances in which already existing or subsequently arising genetic differences succeed or fail.

And that raises an obvious question: was the necessary variation actually there when it was needed?

Popular accounts tend to skate over this. Fire appears. Food becomes easier to digest. Jaws shrink. Guts change. Brains expand. The whole thing can sound almost like an engineering project in which one modification calls forth the next.

But evolution has no engineering department. Mutations do not appear because an organism needs them. Natural selection can favour useful variations once they exist, but it cannot order them from a catalogue.

That is where the cooking story begins to acquire a faint whiff of what philosophers once called pre-established harmony. A cultural innovation creates a new opportunity, and somehow biology appears ready to exploit it.

This is not an argument for Lamarckism. Lamarck famously proposed that characteristics acquired during life could be inherited. The traditional caricature is the giraffe stretching its neck to reach higher leaves and passing a slightly longer neck to its offspring. Modern evolutionary theory rejects that mechanism.

Gene-culture evolution is different. A behaviour does not directly rewrite the germ line. Instead, behaviour changes the environment in which different inherited characteristics compete. If cooking allows individuals with smaller guts to survive and reproduce perfectly well, for example, natural selection may favour biological changes that would previously have been disadvantageous.

There is nothing mysterious about that mechanism. The interesting question is whether we know that this is actually how the human story unfolded. Here the chronology becomes troublesome.

One famous example concerns MYH16, a gene associated with powerful jaw muscles in other primates. In humans the gene became disabled. Researchers have proposed that this change helped reduce the enormous chewing musculature characteristic of our primate relatives, perhaps also removing an anatomical constraint on changes to the skull.

Dating this genetic event is difficult and estimates have been debated, but it may reach back roughly two million years or more. The problem is that secure evidence for habitual control of fire and cooking is much less straightforward at such an early date. Evidence for fire becomes substantially stronger later, while claims for very early controlled fire remain disputed.

That does not prove that our ancestors were not cooking earlier. Archaeological evidence from such remote periods is extraordinarily incomplete. Fires disappear. Campsites vanish. Organic remains decay. Absence of surviving evidence is not evidence that nobody was roasting dinner.

But that qualification cuts both ways. If we do not know when habitual cooking began, we cannot confidently present a precise sequence in which cooking came first and the anatomical transformation followed. The familiar story is therefore stronger as a plausible hypothesis than as a demonstrated historical chain.

There are several ways evolutionary theory can deal with the problem, and none requires mutations somehow knowing what our ancestors needed.

The most important is standing variation. The phrase sounds technical but the idea is simple. Individuals in every population already differ genetically. Natural selection often does not have to wait for a miraculous new mutation. When circumstances change, genetic variants that were already present can suddenly become advantageous.

Imagine a population in which some individuals naturally have slightly smaller jaws, somewhat different digestive efficiency or slightly different metabolic characteristics. Before cooking, those differences might not matter much, or might even be disadvantages. Once cooked food becomes a major part of life, the balance changes. Selection begins rearranging the genetic cards already in the deck rather than waiting for entirely new cards to appear.

That makes the cooking hypothesis considerably more plausible. But it also makes the popular version misleading. The story is no longer simply that cooking produced the biological changes. Cooking altered the selective environment, which then filtered an enormously complicated reservoir of existing biological variation. It has the big assumption that cooking with small jaws led to more offspring, which remains to be proven; it may not result in any significant difference.

There is another important idea: gene-culture coevolution. Again, the terminology makes something fairly simple sound forbidding. Culture changes biology, indirectly, by changing who survives and reproduces. Biology can then change what kinds of culture are possible or useful. The two processes feed back on each other.

We know that something like this has happened in recent human evolution. Dairying created strong selection for the ability of adults in some populations to digest lactose. The cultural practice came first, but it did not magically manufacture the necessary genetic variants. Once dairying existed, individuals carrying variants allowing continued lactase production supposedly gained an advantage in particular environments, and those variants spread.

Cooking could have generated a vastly older and more complicated feedback process of the same general kind. But saying that a feedback process is possible is not the same as reconstructing exactly what happened two million years ago.

The third answer to the cooking paradox may be the simplest: we don't know the chronology well enough. Fossils give us fragments of anatomy. Archaeological sites give us scattered traces of behaviour. Genetic evidence allows scientists to estimate events deep in the past, but those estimates can have substantial uncertainties. Gut anatomy does not fossilise conveniently at all. Meanwhile "controlled fire," "regular fire use" and "habitual cooking" are not necessarily the same event.

Take evidence from several imperfect clocks, each measuring something slightly different, and it is remarkably easy to construct a smooth narrative after the fact. That is where healthy scepticism should enter. The sceptical argument is not that evolution is false. Nor is it that cooking played no role in human evolution. The cooking hypothesis is powerful precisely because it connects several otherwise puzzling features of human biology.

The objection is to turning a plausible explanatory framework into a completed historical account.

"Selection pressure" is not a magic phrase. Naming the pressure tells us why a characteristic would have been advantageous if the appropriate heritable variation existed. It does not, by itself, demonstrate which variants existed, when they appeared, how strongly they were selected, or whether cooking rather than some other environmental change produced the observed result.

In other words, explaining why something would be useful is not necessarily the same thing as explaining how it actually happened.

This is where popular evolutionary stories frequently become too smooth. We start with modern humans, look backwards at the traits that made us successful, and construct a sequence in which each development appears conveniently to prepare the way for the next.

Fire leads to cooking. Cooking leads to smaller jaws and guts. Saved energy leads to bigger brains. Bigger brains lead to more sophisticated culture. More sophisticated culture leads to better cooking. Eventually somebody invents the restaurant.

Viewed backwards, it can look almost inevitable. Viewed forwards from two million years ago, nothing was inevitable. There were numerous hominin populations, changing climates, extinctions, migrations and evolutionary experiments. Most left no descendants. Selection had no destination called Homo sapiens. It merely favoured whatever worked sufficiently well under local circumstances.

That messiness actually provides part of the answer to the apparent "pre-established harmony." We notice the lineage that survived and produced us. We do not experience evolution from the perspective of all the lineages that went nowhere.

Yet a deeper puzzle remains. Evolution cannot explore every imaginable body. Development itself places constraints on what can be built. Genes interact in immensely complicated networks. Alter one system and several others may change with it. Some biological configurations are relatively easy to reach; others may be effectively inaccessible because the intermediate stages would not work.

So perhaps the really interesting question is not: How did the mutations know that cooking had arrived? They didn't. The better question is: Why did the human lineage possess enough biological flexibility for cultural changes such as cooking to push it down such an extraordinary evolutionary path?

That question takes us beyond the children's-book version of Darwinism in which random mutations appear, natural selection picks the good ones, and another rung on the ladder toward humanity is completed. Evolution is not a ladder. Nor is natural selection an engineer. Culture, inherited variation, developmental constraints, environmental change and sheer historical contingency interacted over immense stretches of time.

Cooking may have been one of the most important turns in that story. It may even have helped make the modern human body possible. But "we cooked our food and therefore evolved big brains" is not an explanation of the whole process. It is the beginning of one.

And whenever an evolutionary story sounds so perfect that every development arrives just when the next one needs it, there is a question worth asking: Are we looking at the mechanism, or merely admiring the story we constructed after the event?