A mummified crocodile in the back streets of Oxford might not be an obvious guardian for one of life's great mysteries. But some 2,000-year-old treacle brown remains made up of recycled scraps of Egyptian papyrus, torn up to encase the reptile, hide hard evidence of a substantial historical cover-up. Now stored in 100-year-old kerosene cans and Huntley & Palmers biscuit tins, the ancient fragments were originally dumped as rubbish in ancient Oxyrhynchus (the town of the sharp-nosed fish). Their salvation, by two British archaeologists from 1896, who heard that locals were using the papyri fragments as organic fertiliser, was a godsend: these unpromising shreds rewrite history.

So far just 5% of the million or so fragments have been translated; but they embody the concerns and priorities of the man (and woman) on the street from the first century BC to the fourth century AD. Here is an unofficial snapshot of life at the birth of the modern world. Crucially, this was a time and place where Woman Wisdom, Sophia in ancient Greek, walked the streets. We find her name again and again in Jewish, Christian and pagan papyrus texts. Sophia – a mystical female presence whose appearance is only fleeting in the Hebrew Bible and New Testament – was clearly once a household name and a fixture in everyday lives.

Today we talk a great deal about the perilous place that female opinion and understanding has on the world's stage. The Oxyrhynchus papyri suggest there was a time when female wisdom was foundational to popular belief. Yet Sophia became a casualty of geopolitics. When Christianity developed as the dominant religion of the new Roman Empire under Constantine I in the fourth century AD, it needed "tidying up". Suddenly Christians didn't have just a faith, but a territory of their own. A muscular military structure protected the (extensive) domains of the One True God, and a burgeoning population of (male) scribes and clerics set out to protect the new Christian canon from heresy.

Womanly wisdom, it was decided, needed to recognise her limits – a point succinctly made by orthodox Christian writers: "… she stretched herself forward … until she encountered the Power that sustains and preserves all things, called 'the Limit'…".

There was also a nagging worry that Sophia might be a bit too Jewish. Sophia corresponds neatly to the Jewish Hokhmah. Hokhma is allowed little elbow room in Jewish scripture; but when she appears she packs quite a punch – most notably in Proverbs 8, she is "better than rubies and all things that may be desired … I AM understanding … set up from everlasting, from the beginning … whoso findeth me, findeth life". Hokhma too was a victim of what might be called the "study-hall syndrome" – when a phalanx of scholarly men elected to write the personification of female wisdom out of the centre and into the margins.

Which all helps to explain a conundrum that has long bothered me. At the birth of society and civilisation I find a religious landscape littered with feisty female deities who make wisdom their business. There's Nisaba the Babylonian goddess who looks after the stores of both grain and knowledge in Mesopotamia; the Hindu goddess Saraswati; the Zoroastrian Anahita; the ancient Greek Athena; and the Shinto Omoikane (a fine goddess of holistic thought and multitasking).

But come the end of the bronze age and many of these deities have been demoted. Here we witness a precursor of the Judaeo-Christian scenario. Up until 1400BC, citadel settlements are stable. Goddesses – notably in charge of fertility and learning – have a crucial role to play. But as civilisation gets greedy and society more militaristic, these wise women are edged to the sidelines in favour of a thundering, male warrior god. Just the kind of chap to lead raids on neighbouring citadels – a historical fact we witness in the brutalised archaeology and stockpiles of traumatised human remains: thousands of men whose bones are now emerging from digs across the eastern Mediterranean, north Africa and the Middle East – cross-hatched with axe-cuts, their skulls pierced with arrows, their chests with spears.

The original, Proto-Indo-European, root for wisdom, wid, means to witness, see, spark an idea. Sophia, too, comes from a root that means clear and visible. I think we need to assess this new evidence with clarity – and realise it offers a unhelpfully tenacious 3,400-year-long precedent for our modern lives. Consider this – the prehistoric word for mind – manu – which gives us our word man – originally did not mean a male thing, but instead a thinking thing. I think and therefore I am, a man. As we debate the role of women in society today it is worth reminding ourselves that wisdom – in all its forms – was originally recognised as defining our species, not our sex.

• Bettany Hughes presents The Ideas That Make Us, starting on 27 January, on BBC Radio 4