Organic systems traditionally stress the importance of adaptation through natural evolution along the principle of natural breeds and natural selection. Any marker assisted breeding programme should therefore focus on the use of germplasm from locally distinct traditional seed lines from a particular area or region that are best suited for local weather patterns, soil type and other important agronomic factors when developing new varieties. Maintaining genetic diversity within agriculture is of fundamental importance. It serves as a basic insurance against local crop disease outbreaks becoming regional or national outbreaks. The less diversity in the system the wider and faster new bacterial, viral or other pathogens can spread throughout the national agricultural plant (or animal) base. The use of locally adapted plants which are more appropriate to local ecosystems are important in developing such systems of plant protection based on genetic diversity.

Plant breeding has become such a specialised and centralised industry that this essential diversity has been eroded in recent years. This represents a considerable threat not only to the economy of the farming industry, but also to national food security, human health and the national economy. The Irish potato famine of 1846 is an extreme example of a past national crisis which followed low genetic diversity in cropping patterns. Organic farming reverses this trend of genetic erosion by positively encouraging genetic diversity.

Patent Protection Abuse:
The Soil Association believes that although marker assisted breeding can play a useful role in the development on new varieties, it must not become a means to patent specific genes and that access to genetic information provided by the technique must be made available free of charge to all scientists requiring it for research purposes. Experience with the human genome project has already shown that the biotechnology industry frequently seeks to patent the genes it discovers through mapping research, particularly where genetic sequences are believed to be linked to commercially exploitable traits. The Soil Association believes that this is immoral. It contravenes the most basic of traditional patenting principles, which allow patents on inventions made by humans, but not discoveries in nature. If novel traits identified by genomic discovery are allowed to be patented this potentially sound technology will be abused, restricting access to scientific knowledge of naturally occurring biological phenomena by others for the benefit of the wider community.

Genetic Engineering - The dangers:
Genetic engineering involves the artificial insertion of individual genes from one organism (typically, but not exclusively, from other unrelated species) into the genetic material of another. This methodology is the cause of much concern. Scientists have identified particular effects that some specific genes have on the characteristics of an organism (e.g. the identification of a gene in a plant which makes it resistant to a particular insect pest). However, wider effects may occur through different genes interacting with each other. At present, these interactions are not well understood by scientists, or even understood at all in many cases. The artificial introduction of novel genetic material out of context using recombinant DNA in this way is fraught with difficulties given the depth of such knowledge deficits.

In addition the very process of genetic engineering increases levels of risk by by-passing the integrated bio-regulatory systems inherent and generally conserved in the sexual breeding process. In nature genes are regulated by neighbouring (and sometimes distant) DNA sequences which, for example, control when or where in the plant the gene should operate. These processes have so far only been identified and understood to a limited degree. As a result current agricultural genetic engineering techniques are unable to take these fundamentally important relationships into account when creating new organisms incorporating recombinant DNA. Equally in the genetic engineering of plants little or no control is exercised over the locational placement on the genome of inserted genes. Placement is essentially random and multiple copies may also be inserted unintentionally.

Because of this lack of knowledge of the natural regulatory functions within plant genomes, as well as the random positioning of inserted foreign genes, unpredicted side effects occur routinely with genetic engineering techniques. Many of these have been recorded even in commercialised varieties. This approach can lead to dangers such as allergenicity, the creation of new toxins or poor agronomic performance. An example of an unpredictable physical side effect was reported in the New Scientist, whereby more lignin in GM soya than non GM soya was found, causing stunted, weak stems which split open and reduced yields. By contrast, however, when Marker Assisted Breeding is used to assist traditional sexually-mediated breeding programmes, natural processes of gene regulation and placement are not by-passed. This avoids exposure to the novel health and environmental risks inherent in genetic engineering plant breeding methods .

Organic Farming:
It should be noted that the principles of organic farming revolve essentially around animal and plant husbandry rather than merely the attributes of a specific variety. "The base line of the investigations [of seed varieties] of the future must be a fertile soil. The land must be got into good heart to begin with. A valuable method of testing our practice is to observe the effect of time on a variety. If it shows a tendency to run out something is wrong. If it seems to be permanent, our methods are correct. The efficiency of the agriculture of the future will therefore be measured by the reduction in the number of plant breeders. A few only will be needed when soils become fertile and remain so." Sir Albert Howard, An Agricultural Testament, 1940

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