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The UK PhD programs are based upon just research for three years, whereas in the US there tends to be substantial graduate course work included.

How does this difference affect the quality of the PhD thesis, and the quality of work produced in the long term?

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You realise that the main difference is that in the UK the undergraduate programs are more specialised, so to some degree US students are playing catch up in their coursework. –  Dave Clarke Feb 6 '13 at 18:12
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When someone earned successfully and honestly his PhD in a good research group, either in the US system or in UK/Germany (Master degree is often mandatory for starting PhD), there will probably be no strong differences in the overall quality, I wouldn't make here any generalizations based on this fine system nuances. The level and depth of research experience are very similar (also STEM students in Germany don't work on average 80-90 hours a week, 60 will be rare ;))

But, when a student did choose a distinct topic and research field for his master and PhD thesis, you can be a bit more sure he is really motivated for this work and research generally, while a US PhD student with a bachelor (and without master) maybe is just trying to finish what he started over the years, in spite of vanishing interest/motivation in research generally (see link above) or that distinct topic. During the short time of a bachelor thesis you cannot find out, if you are suited for research and a distinct field in my opinion. In Germany it's hard to get invitations to PhD job interviews at all without a master thesis near to a given research project. Motivation and background is here more important than 0,5 better grade or 3 year younger age. In interviews they mostly check, how motivated, interested, knowledgable is a candidate for that distinct field. So there will probably be no big differences in quality, but you can be more sure about long term motivation and therefore originality/quality of his research.

As we currently have a (another) case of plagiarism in Germany (our education minister obviously wasn't trained, e.g. by a bachelor nor master thesis, for writing a long PhD thesis correctly), I have to add that somebody who has written a bigger master and PhD thesis will also have more practice in publishing, citing, researching literature...

Side note: Personally, I think the german system is more selective, while the US system can afford this system because of a abundance of PhD students and applicants (thats also the reason they have to work 80-90 instead of 60 hours, competition being stronger and teaching of undergraduate students in Germany needs very good command of german language, we are limited in hiring foreign students for those jobs). A very good master and PhD thesis is a strong hallmark for the motivation of a student and future researcher for a distinct research field.

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In the UK, you can normally do a PhD only after completing a master's degree, i.e. you begin with research after you have already done a year or two of graduate level coursework. In the US, graduate studies normally begin begin with courses and end in research, at the end of which you have obtained a PhD. You can enroll directly after your bachelors studies. Overall the two are quite comparable in terms of time spent in courses and on research once you have your PhD. There are exceptions of course, but I understand that this is the default situation.

The effect on the thesis itself probably depends on how closely related the courses are to your research topic. In my experience, research topics are usually about adding new knowledge to a field, so it's hard to find more than a few courses (if even a few) that overlap much with your research. I see courses more as a way to gain some general expertise in your field.

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In my opinion, there is an effect but it will only become apparent in people who would be borderline cases anyway.

In the short run, a given project- be it dissertation or what comes after- will require a very specific set of skills that, in general, need to be acquired on-the-job. However, if the grad school courses are relevant the PhD program with coursework will have a slight advantage. (I'd love to find these programs with useful prerequisites.)

In the long run, the challenge shifts to choosing the right projects. That requires a broad perspective that classes in grad school could give.

A motivated person who lacks the formal coursework can catch up.

Given all these, I think that the difference in PhD programs will only hurt those graduate students who might lack the motivation for life-long learning anyway.

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The courses on research methodology greatly improved the value I got from my PhD. Sure, you can make it through yourself to get the research done, but a PhD implies having research skills and deep understanding of the scientific method, which can be taught formally. Tough US-style courses can only benefit. That said, I experienced a massive difference in the quality/relevance of PhD courses.

I also have a beef with the German PhD system (in reply to another post here). At least in my own field (social sciences), many German practitioners do a PhD in 2 years (often part time) by writing a "big book" which is defended in front of one's own adviser plus 1 external (generally). There is thus a glut of PhDs in the workforce but few if any German PhDs publishing in my field in ranked journals. Fortunately I think this is not the case for STEM subjects where the level is excellent in Germany. Still, the pressure to be "Herr Doktor" in order to move ahead in a political or management career in Germany seems to have lead to many low-quality dissertations written on the weekends with no formal teaching support (hence all the intentional or unintentional plagiarism popping up recently in Germany). Where there are PhD courses, there is support and structure, a research community, and a greater likelihood of higher quality and understanding.

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