Having read the first three pages, I see the usual mistake of laymen thinking in terms of laymen's English. Like with the legal profession, language in science has exacting definitions that don't always match laymen's English.
For example, to Bob down at the bar, a "theory" is pretty much just a wild guess, mostly or entirely unsupported by data.
In scientific terms, a "theory" is an extensively tested idea with a large body of supporting evidence. It is the highest, most certain place an idea can reach in science.
