Historically where did all of these different forms arise, and when are they used? I noticed that だ and である both have their place in different 文法形, what is the difference in their meaning? I know that in things like 論文 as well as, apparently, on Wikipedia である is used, but I really don't know why.
だ is a reduced form of である, which is itself a reduction of にてある (the particle で was originally にて). です is a reduced form of であります. As far as we can tell, the copular verb ('to be X') in Japonic has pretty much always been locative particle + ある. In Old Japanese it was なり (a reduction of にあり, back when あり was the 終止形), and in the Ryukyuan languages it tends to be something similar to ya- (probably にあり minus the n instead of the i). Pretty much all of Japanese has since replaced the に with で, but depending on where you are である can be reduced to any of だ, や or じゃ.
である tends to sound more formal and literary than だ/です. My guess is that its usefulness derives from the fact that sounds neither informal (like だ would be) nor deferential (like です would be), and is thus a useful alternative when 'talking to nobody', as it were - you'd use it when writing some sort of impersonal work (non-fiction or maybe third-person-narrator fiction), you'd never use it when speaking.