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How Do I Choose: A Program, An Advisor, A Topic ?

The most important choice you will make is your thesis advisor (mentor, supervisor, head of your dissertation committee). This matters more to your future than your thesis topic or even the name of the degree you get (university, department, or program).

The most important practical quality in an advisor is that s/he be nationally or internationally known and respected in the field; the more famous the better. Such a person will probably have little time to give you, so you will also need other, even unofficial guides and advisors (who can also be members of your committee). This person's recommendation is often worth more than your dissertation or degree in getting a job, getting research funding, making key contacts at conferences, etc. He or she is your social entree into the field. Their stamp of approval counts for a lot with all the many people who know (but would never admit) that they really can't judge quality or originality in the field. Do not, however, yourself pay any attention to such recommendations given to others; they mean very little in terms of research quality.

Beyond reputation and power, the other qualities to look for in an advisor are (1) a reputation for getting dissertations students "out" -- meaning graduated -- in a reasonable period of time (less than 5 years); (2) someone who is at the forefront of the field and knows what is going on nationally and internationally; (3) someone who fits with your own preference as between: telling you what to do vs. letting you work things out for yourself. Your advisor may or may not be the person you actually learn the most from. You should also be on the lookout for (1) really insightful people in the field, and (2) people who can teach you technical skills. The first sort will give you ideas about where what's worth doing and where the field ought to be headed. The second sort will enable you to actually get something done. 

If you can combine a thoughtful and caring mentor, a brilliant scholar, and a person with power in the field in the same human being, that's the ideal. Realistically, however, there are just not enough such people to supervise all doctoral students. Faculty choose their doctoral students. You have to get to know the person you want, and you have to have something to offer them -- energy, time, hard work, intelligence, ideas, a different viewpoint, special experience, access to data or sites, your own funding, an engaging personality ... but something.

Your thesis topic matters less than you suppose. Very few people are hired on the basis of their specific dissertation topic. The general area or specialized subfield matters more.You should pick something that (1) can be completed with certainty in less than five years, (2) is currently regarded as topical and important in the field, and (3) is interesting enough to you that you can live with it night and day for at least a few years and maybe longer. As you plan your dissertation, think long term: Will this be publishable with only slight modifications as my first book? Will I be easily able to extract 2-3 good, substantial publishable journal articles from this work? The book plan is better; you can get the articles out (usually after graduation, occasionally before) while preparing the book. To get the book published these days, you will need to be able to identify a market for the book: what large group of people will be interested? Think ahead this far when choosing your topic. (This advice matters mainly to you if you are looking for a tenure-track academic job. Otherwise, you should consult with senior people in the field of work you are really aiming for and get their advice about topic choice, publication, etc.)

Finally there is the matter of a program. It does matter where you get your degree (see above), and in what field or program. Certain universities and departments are known for certain specialties. If helps to find out about this before you choose a program. If you have a choice among departments: old and established departments tend to be more conservative, more influential, and more riven by internal politics; newer ones are the reverse, but are fanatical about the appearance of having high academic standards. It is often easier to get a job with a degree in a traditional discipline rather than in a new field or interdisciplinary program. You can study the new fields and do interdisciplinary research without putting it on your diploma. (I happen now to head a new, interdisciplinary doctoral program. It is not meant for people who want to become narrow specialists in one subfield; they would do better in a more traditional program.)

The most important consideration in choosing a doctoral program is the faculty, not the curriculum.
Coursework is a small part of doctoral education. It also matters less whether the faculty are excellent teachers; doctoral students are expected to be very self-reliant, to know how to learn on their own with only general guidance from the faculty. This is less true in the U.S., more so in  Europe. Find a program whose faculty includes at least two or three people you might consider as mentors or supervisors, well-known specialists in your area of interest, or broadly knowledgeable scholars who can guide your development as a researcher. And avoid departments where there are strong rivalries and conflicts between different factions. Students usually get caught in the middle. Choose a program where many viewpoints are represented, but not one where the faculty are at odds over their basic standards of good research or their basic views of what is important in the field.