TITLE: Books on the History of math research at European universities
QUESTION [6 upvotes]: Are there good books that cover the history of math and mathematical science (ex. physics, chemistry, computer science) PhD programs in the Occident? My primary motivation is to figure out how the PhD system developed into what it is today. 
Note: I will probably start a PhD focused on theoretical neuroscience in 1.5 years.

REPLY [5 votes]: I asked a more general variant of this question on Twitter: Might there be really good books on the history of science and technology PhD programs in the Occident? which was answered by Eli Shlizerman, who runs a lab focused on data-driven dynamical systems at the University of Washington. The History of University in Europe comes in four volumes which have pretty good ratings on goodreads:

The Universities of Europe in the Middle Ages - Volume 1
A History of the University in Europe: Volume 2, Universities in Early Modern Europe (1500-1800)
A History of the University in Europe: Volume 3, Universities in the Nineteenth and Early Twentieth Centuries (1800-1945)
A History Of The University In Europe, 4 Universities Since 1945

I also found two other texts which might provide good background reading on the origins of the modern scientific research university: 

The Rise of the Research University: A Sourcebook
Academic Charisma and the Origins of the Research University

Together, I think these texts might complement the references listed by Dr Beenakker. 
Note: There is one approach to this question raised by Konrad Kording, a neuroscientist, that is probably particularly insightful. On Twitter he mentions that very little was happening in Europe around 1000 AD while Ibn al-Haytham wrote excellent books on optics. Two centuries later Paris started handing out PhDs. I am currently looking for a text that focuses on this sequence of events.