Is there a (text)book on how academia works? Is there a (text)book on how academia or science works? What I'm looking for is not anecdotes and tips, but actual insights presented systematically, like any textbooks in every disciplines. This book should provide connections between varieties in academia, and how the root of seeking new knowledge shaping the varieties as they are now. I think this can be categorized as an application of sociology.

Some questions I want to know:


How does a new theory spreads out and be accepted? 
Can it answer everything? 
How do governments fund researches? 
[to be added]


Meta discussion: How to make the question asking for books on academia/science not a shopping list?
The study of the higher education and academia is a huge area of research, and I must admit, I am no expert in it. While some publications are opinion-based, as Massimo Ortolano notes in his comment, there is a growing number of research-based works on academia developed within different disciplinary frameworks, which includes those developed within the framework of academic sociology, as you mention in your question. 

Among the trailblazing works in the sociology of academia were the publications by R. K. Merton, and also
R. Whitley, The Intellectual and Social Organization of the Sciences (1984), and P.  Bourdieu, Homo Academicus (1984), focusing on French academia. 

Among the recent notable books in this field, I can cite M. Lamont, How Professors Think: Inside the Curious World of Academic Judgment (2010), based on a study of US grant peer review panels, and 
J. R. Posselt, Inside Graduate Admissions: Merit, Diversity, and Faculty Gatekeeping (2016), based on participant observations about a number of graduate admission committees at US universities. Tracing the differences between the branches (varieties) of academia and explaining them is a major theme in both these books. But there are many more.