In the comments below there is a lot of talk about the worry of transferring gene X from organism 1 to organism 2, where the two organisms are very far apart on the tree of life. I’m a little sanguine about this, but that’s because there is already much of this going on through natural processes.
Carl Zimmer for example points out that 8 percent of the human genome seems to derive from endogenous retroviruses (the post draws on material from his book A Planet of Viruses). This is probably a low bound number, as he notes in the comments. Additionally, this isn’t just limited to viruses. See: Horizontal gene transfer between bacteria and animals.
I think on of the chasms between geneticists and the public is that a lot of things that seem creepy and strange to the public are part & parcel of the geneticist’s professional toolkit. For example, to my knowledge no transgenic mice have turned into the Brain. I have friends that order weird mouse varieties, and then do weirder things to them, every week.