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In biology, there are always exceptions. As you pointed out, viruses frequently mess around with genomes. Also, some bacteria can grab a plasmid from a completely different species of bacteria. Larger critters can’t pull off tricks like that, and that’s the group we usually think of.
Totally agree about gene editing being neutral. It’s just a tool like any other. That doesn’t make it good or evil. People who use it get to decide how it’s being used, and that’s the step where things can go wrong. It’s a powerful tool, so when used correctly, the results are life-changing. When mistakes are made, the price can be very high.
What about the terminology then? My previous examples are usually covered under evolution, not genetic manipulation, and I think intention is the key difference. Evolution happens on its own, while editing requires an intention.
I think evolution also covers selective breeding, which is intentional too. The "natural" form is natural selection. I think "Genetic Engineering" is the best term for the lab process. It's not ideal, because I'd argue selective breeding could still be argued to be genetic engineering, but it's the most accurate I think that exists. Engineering does imply a certain amount of control that could be argued isn't met by selective breeding. Genetically modified organism (GMO) is a horrible term, though that is probably the most common term for the lab process.