In prepping the soil, rocks were removed, chalk and coal ash were added to various areas & trees were planted. Darwin would kick bits of flint (removed from fields) at each turn, as a sort of way of keeping track of where he was. He noticed, absently, that the flints became harder to find in time.

It was Polly who solved the mystery of the disappearing flints. when she dug a hole nearby. Darwin was surprised to find a layer of flints several inches under the soil. There were layers of soil on top of the chalk & coal ash, too. Something was adding dirt. The plot thickened! (dad joke)