The Energy Bulletin had a fascinating post on modern soil science and management. There is so much we don't understand about how we grow our food, yet so few are willing to question the practices. It sounds eerily like Peak Oil and the way we use energy...
"Magic" is how humans have customarily described the soil's natural cycles of decay and growth. Without a scientific understanding, our ancestors relied on observation and traditional practices to grow crops.
Modern chemical agriculture has been only marginally better at understanding the soil. Unable to control the natural cycles, it bypasses them with synthetic fertilizers and pesticides. Despite the outward successes of modern agriculture, its heavy-handed approach brings with it pollution, soil degradation and other ills.
In contrast, organic methods like permaculture have attempted to work with natural cycles. Despite the many insights and successful practices that have emerged, a rigorous scientific model is still lacking. Permaculture and its brethren are accused of being belief systems rather than science. It's hard to make progress without having a common understanding of how things work.
Recently, however, soil ecology has developed to the point where we can open the lid on the black box of underground processes. We can begin to understand how micro-organisms maintain the structure and fertility of the soil. We learn that symbiotic relationships between plants and micro-organisms are not the exception but the rule.