Through the industrialization of agriculture, the productivity per unit of land and per farmer effort has certainly been increased. But this has been achieved by increasing energy inputs, particularly in the form of fossil fuels for machinery and the production of fertilizers and pesticides. Simultaneously there has been a major increase in pollution, in soil erosion and other related phenomena. The energy efficiency of the agricultural system has dramatically decreased. Agriculture has become an energy sink. Furthermore the natural capital of the agricultural system has decreased in several ways. Soil fertility has decreased resulting in increased dependence on synthetic fertilizers. The natural pest control capacity has declined resulting in increased dependence on synthetic pesticides. The amount of genetic material in the gene pool is gradually eroding away as it is specialized to a narrower and narrower range of crops.
The modernization of agriculture, as currently envisaged, has a marked tendency to enrich a limited number of wealthy landowners who can afford to invest in high-yield seeds and who can afford the expensive fertilizers required if such seeds are to perform satisfactorily. When these farmers prosper, they then buy out poorer farmers or terminate the leases of peasants on their property in order to expand the cropped areas. Such modernization has therefore been a major factor in increasing the number of landless peasants and encouraging migration to urban slums. In addition it has increased dependence on imported technology and on imported energy (to operate the mechanical equipment). The final agricultural products tend to be more expensive than those produced by traditional methods and consequently become too expensive for poor people to purchase.
The first coffee plantations in Central America had been incorporated into natural forests by carefully thinning existing tree cover and selectively clearing ground vegetation. Original vegetation, including nitrogen-fixing leguminous plants, had been left basically intact. The combination of shade trees (including planted banana and citrus) and coffee trees not only ensured richer and more complex agro-ecosystems, but larger trees also served as efficient soil stabilizers on the moderate to steep slopes which are predominant in the coffee growing regions of Costa Rica and El Salvador. Moreover, a forest-like appearance was regained within a few years when the coffee seedlings matured into trees. In the mid-1970s, shade trees were razed and other non-coffee vegetation cleared in coffee plantations in Costa Rica in order to enhance the coffee trees' productivity. More efficient (high yield) coffee varieties were planted. Although modernization practises increased the yield in the short run, they proved to be ecologically counter-productive. Direct exposure to the sun accelerated photosynthesis of the trees which, in turn, led to rapid soil exhaustion. Moreover, the removal of native nitrogen-fixing leguminous plants necessitated increased dosage of nitrogen fertilizers. Loss of the protective natural cover and of mature root systems hastened soil loss by wind and rain, and produced a heavier sedimentation load in nearby rivers. A parallel system for cocoa plantations, called the "clear-cut system", was introduced at about the same time into Brazil and Costa Rica (where practically 90% of forest in the middle altitudes has been eliminated by coffee plantations); however in Brazil, the traditional cabruca plantations of cocoa (clearing substrate vegetation but retaining some indigenous tree cover) remains the most common and is considered by many to be the most environmentally positive form of agriculture practised in Brazil today. In Costa Rica, low interest credit is now being offered to coffee planters who combine commercial shade trees with coffee plants; there has also been discussion about the possibility of using reforestation incentives to plant trees in existing coffee plantations.