Now the mystery may have been resolved.
Gert van Tonder, a postdoctoral fellow of the Japanese Society for the Promotion of Science at Kyoto University, and Michael J. Lyons, a senior scientist at ATR Media Information Labs in Kyoto, applied a shape-analysis technique that can reveal hidden structural features to the garden's empty space.
Earlier studies of how humans and other primates process visual images suggest that we have an unconscious sensitivity to the medial axis of shapes, said Van Tonder.
"Imagine starting two fires in a field of dry grass," he said. "Where the fires meet, at points equidistant between the two starting locations, is the medial axis."
His analysis indicates that the same unconscious sensitivity is able to discern the image of a trunk and branches of a tree within the Zen garden's pattern of rocks and stones. Viewed from the verandah, the image is apparent to the subconscious but is invisible to the eye.
The authors conclude in a report published in the September 26 issue of the journal Nature that the unconscious perception of this pattern is the source of the garden's calming effect.
If the rocks were to be rearranged, the invisible tree structure is lost, they say.
Van Tonder believes the garden's designer intended to create the subliminal feature—demonstrating an understanding of the physics of the human eye and subconscious hundreds of years ago.
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