Dear Johannes

 Is it different in Ruhr-Universität Bochum? Is there PhD (not dr. med) program by medical school?

Dr. Dietrich described the situation well. Discussion in English should be avoided, though, because phonetically similar terms may have very different meaning.

In Germany, an "agency" (actually the Chamber of Medical Professionals = Ärztekammer)  that is invested with appropriate authority by the State, certifies an academically qualified person for "practising medicine" (= license to inflict harm on a patient for the patient's benefit, in very simple words).  This is simply a professional qualification that invests the legal right to call oneself  "Arzt / Ärztin". Informal communication in German will also have "Herr Doktor" to address an "Arzt" and "Frau Doktor" to address an "Ärztin" - from the point of view of a patient or other health professionals (e.g. nurses, officials). Within the medical profession, one can only use "Herr Kollege / Frau Kollegin", though.  A polite medical professional (Arzt / Ärztin) will address his/her colleague as "Herr Doktor / Frau Doktor" if and only if he /she has in addition the academic degree of "Dr. med. (dent. /vet.)" that is given by the Medical School (Medizinische Fakultät) of a state-approved German university.  In conclusion, I advise against translation into English as "MD" since it is only adding confusion. 

With this background, two points have to be made first:

First, German Science Foundation (Deutsche Forschungsgemeinschaft, DFG) accepts research funding applications from academically educated individuals with  qualification of "Dr. (med./ dent. /vet. / rer. nat. / -Ing, phil. , ...)" . This will not apply to "Arzt/Ärztin" since this is only a professional qualification, while "Dr." is an academic qualification and a certification by which an academic school (Fakultät) testifies a person's ability to conduct directly responsible research  (Forschung in eigener Verantwortung). A note in passing: This is not to be expected from anglo-saxon type PhD programs that serve to "push a waggon on the program's tracks".)

Second, some German Schools of Medicine (Medizinische Fakultäten) offer "Dr." qualification for researchers who are not certified to practise medicine - not Arzt / Ärztin, but still work in the medical field, e.g. physicists, mathematicians, biologists, etc.   For example, at Essen Medical School, there is "Dr. rer. medic.", in other places,  there is "Dr. sc. hum. biol." - all this is at the discretion of a university's medical school.

Now, to answer the two questions:

Question 1 (3 d ago = 04 March) :  In Germany, any Arzt / Ärztin may do clinical bed-side research - without direct funding from DFG, though. But actually, only Arzt/Ärztin is permitted to do clinical bed-side research = research that involves patients in a hospital! However, direct funding of directly responsible research may not be granted to Arzt/Ärztin without Dr.med.-title.

Question 2 (1 d ago = 06 March):  By the Bologna process, so called "PhD Programs" have been implemented at all Medical Schools (I assume). However, these address the established "Dr. med." schemes and are just called "PhD" because of the English / European terminology, but they do not imply that it is accessible for non-Arzt/Ärztin.    

Note in closing: I do not discuss the comparability of "Dr."-titles granted by different schools (Fakultäten) from the point of view of scientific merits, because this cannot be compared well and academic schools have the right to set their standards. It is not fair to discredit the work of a person who complies with the standards of his / her academic environment.

I have many times been in Germany as a scholarship recipient of the corresponding German government and in hospitals (University Hospital) where I stayed, I got the impression that I believed in the fact that there are programs for the title of PhD.