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This is in contrast with genetic engineering, where the genome is directly modified by humans. There are not the biological checks and balances present in the creation of a genome modified in a lab, as there are in nature.
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Direct modification overcomes some barriers, yes, but I'm not aware of any evidence that suggests that overcoming these barriers presents any kind of a danger to the organism or to other organisms, beyond traditional selective breeding. Traditional selective breeding also overcomes many natural barriers and it alters genomes far more than simple insertion of a gene by genetic engineering.
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Genes often operate not singly, but in a network of other genes. What is more, these networks aren't really understood - there is a great deal of work being done on gene networks in simple organisms, but large scale gene networks in complex organisms like people are not properly understood. The consequences of manipulating these gene networks is difficult to predict without much greater research.
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And traditional breeding modifies these networks far more than insertion of a single gene by engineering techniques. Traditional selective breeding can completely break these networks apart, and take a selected line all the way to the limits of functionality. This has been known since the 1920s.
So if someone is worried about interfering with these networks, it seems to me they should be far more concerned about traditional selective breeding than by insertion of single genes.
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I take it you're also more generally refering to antibiotic resistant bacteria, and 'People' are still very worried.
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Sure they are, because of natural selection in human populations in which antibiotics are overly prescribed. It's the selection that people are worried about (or should be worried about) not the mere existence of such resistant variants. It's not genetic engineering per se that's the problem, since these variants both exist naturally and can be created by either traditional means or by genetic engineering.