Paleodictyon

Paleodictyon is a fairly common fossil that goes back at least 500 million years. It consists, as you can see, of an array of hexagons. They form in marine mud, mostly in very deep water.

Scholars have been wondering what created these patterns since the Middle Ages; here is Leonardo's drawing of a specimen he saw. When a professional paleontologist first described the fossil around 1850 it was thought that these represented the burrows of some unknown soft-bodied creature. Modern speculations have focused on either some kind of sponge, perhaps a glass sponge (some of those have hexagonal skeletons) or else one of the giant, single-celled organisms called xenophylophores.

Then, in the early 2000s, scientists exploring the Atlantic's Mid Ocean Ridge found something quite remarkable: modern, apparently living examples of Paleodictyon. You might think that this would solve the puzzle, but no. Sampling of these patterns produced no living organisms except for bacteria. Were they all abandoned? Or were they produced by an organism that spent most of its time elsewhere? There are even weirder theories, for example that they are bacteria farms created by some organism that deposits its wastes into these holes, then feeds on the resulting ecosystem. 

Fascinating that these common expressions of life's bountiful weirdness remain so mysterious despite all the science that has been thrown at them.

11-minute PBS video, wikipedia