In「である」、my previous understanding was that the「で」functions the same way as the "method/means" particle「で」by making everything that came before it attached to「で」and that「ある」is just regular「ある」just like usual.
However, I have been told elsewhere that this「で」is a copula. This begs the question as to why it is before「ある」。 Furthermore, whenever I see a chart of です conjugations, I don't see「で」on it. So, is the「で」functioning as a copula for the preceding portion of its clause? If so, then why is it not「だ」？
I also have a comprehensive Japanese Linguistics book here, but its explanation (while extremely thorough like a legal text) does not describe how it works.