Natural Agriculture guidelines explain that methods currently used in conventional farming misinform farmers about the cause of crop damage, which leads the farmer to feel that the only way to control crop problems is to apply more fertilizers, or spray more pesticides or fungicides on them. This misunderstanding creates a cycle of increased damage and increased preventive inputs. When inputs are no longer added, the unnatural elements in the soil decline and the soil will recover its health and regain its power to regulate natural processes. Plants, in turn, increase their vigor, extending their roots deeper into the ground. They grow disease-free, becoming resistant to pest or wind damage and resilient against any other natural change. The most remarkable phenomenon is that through this process, the flavor and nutritional value of the crops are increased.

The essence of any agricultural production system, especially Natural Agriculture farming, is the primary focus on achieving the most fertile soil where the soil will produce the highest quality and quantity of agricultural products. In conventional agriculture, this is done with the addition of inputs such as fertilizers and manures, soil amendments, and tillage practices. The problem with this process is that effects are short lived and need to be repeated on a continuous basis to sustain the desired improvements. This also incurs input costs and labor requirements.

Mokichi Okada wrote about the Law of Purification. This concept focuses on spiritual aspects of Natural Agriculture especially related to soil quality. This law has a premise that all applied nutrients accumulate as hidoku, or fertilizer poisoning.  This can be compared to spiritual clouds or the degradation of a soul. In this regard, pure soil is degraded by applying fertilizers and other chemicals, and even by applying any compost, as Natural Agriculture farmers notice at later stages of their practice. These inputs contaminate the soil by causing the soil to be imbalanced. As the amount of hidoku or toxicity accumulates, both in the seeds and the soil, the soil decreases its ability to exhibit its full potential. The hidoku layer forms just above the subsoil layer (A). Hidoku can be remediated by absorption through root systems and discarding the plants (B) or through plowing the field deeply to break the hidoku layer ©. In fact, crops grown from purer soil represent purity and grace of the soil and seeds. After hidoku is eliminated from the soil, the plants regain their ability to absorb nutrients in the soil and produce healthy growth.

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