Most halogenated organic compounds are toxic, but I know that the thyroid produces hormones that contain covalently attached iodine. Are there any other halogenated organic compounds produced by humans or other organisms? I’d imagine there are a variety of bacteria that can metabolize such compounds and probably some that can synthesize them as well.
Here and here are a few sources for that. Bacteria, algae, lichens, sponges and coral are some of the major sources.
There’s an important distinction to make here - which halogenated compounds are toxic is pretty predictable. In the case of the thyroid hormone, you have iodine attached to an electron-rich aromatic ring - these iodines will not do any sort of substitutions (S[sub]N[/sub]2, S[sub]N[/sub]Ar) which are normally associated with toxicity. Halogenated compounds aren’t toxic because they’re halogenated, they’re toxic because they’re reactive.