If your biological attack removes your own pawns they are not scored as clearly stated on pg 8.
Does the same spply to Nukes ? I cant see it specifically stated and you normally score 'nuked' population as per point 1 at the top of pg 9
the only time I can see you "might" Nuke your own population is as the Arab Caliphate when someone controls Central Asia with just one marker. It doesn't seem a likely option but it would be nice to confirm how it should work