Polite request to evaluate whether "emboss" is appropriately switched on in the default desktop profile. I haven't seen any package requiring it in ::gentoo, which suggests that users could live without it or activate it locally if required.
I don't particularly use applications related to emboss, so disabling it in my systems yielded no changes.
Its addition seem to date back to 2005 (bug #82428), and from a quick look only see 6 packages are still offering the USE:
There was an attempt to get it removed before (bug #138822), even if harmless not sure I agree should keep very-specific hardly used (anymore) clutter in global defaults.
(In reply to Ionen Wolkens from comment #1)
I tried `emerge -p` all these packages with -emboss and they would install gracefully, without the flag of course.
I am assuming that if we don't have emboss at all in global defaults, those packages will revert to whatever they have in IUSE (e.g., aaindex will enable emboss).
Sadly, bug 138822 doesn't really explain the rationale of why this wasn't done before :(
[Tentatively assigning to sci-biology, but they aren't the only people who could answer this.]