Are you saying the bible does not state that the clean and unclean entered the ark two x two? Which bible are you reading?
1. The Bible is an account of miracles that defy the laws of physics. There is no way to disprove a miracle using scientific tools.
2. The Bible is primarily a spiritual book and it must be understood from a spiritual perspective. The use of the word "kind" and "sort" does not have to fit in with the ever changing definition of the word "species". They are two different things.