Well, yes and no. It's true that traditional breeding, purposely growing plants or crossbreeding them for certain characteristics, can be a messy business. Since plants often exchange large, unregulated chunks of their genomes, breeders may end up getting unwanted traits along with the ones they're seeking. For example, potato varieties created through conventional breeding sometimes produce excessive levels of chemicals called glycoalkoloids, which can be poisonous. And it may take many generations to get the characteristics that breeders are trying to achieve [source: University of California San Diego].
Genetic engineering is a bit more systematic. Basically, scientists extract DNA from one organism, copy the gene that's responsible for desired characteristics — called a transgene — and then put it into another organism. They do this either by inserting it into a bacteria and infecting the organism with it, or by using a gene gun, which shoots microscopic gold particles covered with copies of the transgene into the organism. Since they can't control whether the transgene inserts into the recipient's genome, it can take hundreds of attempts to get a few GMOs [source: University of Nebraska -Lincoln].
But there is one really significant difference. Genetic engineering can produce much more radical changes in plants and animals than selective breeding ever could. Scientists, for example, have implanted monkey embryos with a jellyfish gene to breed monkeys with glowing green feet [source: Coghlan]. It's not hard to imagine how the power to create a plant or animal with freaky characteristics could be misused, either accidentally or on purpose.