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)

He observed that earthworms were leaving tracks at about the same levels. Measuring carefully in pits dug by workers (not Polly), he determined the worms were adding their feces/castings at a rate of 0.22 inches a year. From this, he began an intensive study of earthworms.