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Nontarget effects of gene manipulation
State Line Observer, January 26 2009,com_mojo/Itemid,90/p,3760/
A chief concern of those critical of genetically modified foods deals with unintended consequences or nontarget effects:

"when foreign genes are introduced into an organism, creating a transgenic organism (commonly called a genetically modified or genetically engineered organism), the results for the organism and its environment are almost always unpredictable. The intended result may or may not be achieved in any given case, but the one almost sure thing is that unintended results - nontarget effects - will also be achieved."

The Nature Institute maintains a website dedicating to tracking the nontarget effects.
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Some examples:

canola_004: Pigs fed GM canola had reduced daily weight gain and the canola had higher concentrations of undesirable substances.

maize_002: Atlantic salmon fed Bt corn had altered enzyme activity in liver and intestine as well as altered proportions and numbers of different white blood cells.

pea_001: Mice fed with transgenic weevil-resistant peas showed immune reaction while pigs and chickens had reduced starch digestion.

potato_002: Inulin-storing potatoes had higher alkaloid content and pigs fed on them had reduced daily weight gain.

soybean_002: Diet containing glyphosate-resistant soybeans affected the nuclei of liver cells in mice.

The Nature Institute asks, Do we really know what we're doing?