The difference, it seems to me, is between soil that is alive and soil that is essentially "dead." I want my food to come from living soil.

Have you hugged your pet Nematode today?

See the wikipedia entry on one subtle aspect of the relationship between living soil and plants:

Plants grown in sterile soils and growth media often perform poorly without the addition of spores or hyphae of mycorrhizal fungi to colonise the plant roots and aid in the uptake of soil mineral nutrients. The absence of mycorrhizal fungi can also slow plant growth in early succession or on degraded landscapes.

http://en.wikipedia.org/wiki/Mycorrhizal