Hi,
I'm a soon to be graduate of the MD/PhD program and I want to rebut the statements made by the person you spoke with in the strongest possible terms.
Was this individual trained at Rockefeller before 1985? This is an important bifurcation point in the history of the institution. Before this time, there were no junior faculty as heads of labs--they could only be found within a professors empire. And I emphasize empire. Previously, RU labs were notorious for their insularity because the labs were organized in a highly vertical structure. Then, the lack of departments served the interests of powerful professors who elected to not interact much. The best example of this thinking is the Weiss research tower. Built in the 1970s, this building was designed with independent heating/cooling for each floor. THis was, as one faculty member put it to me, so that if the person the floor above or below you was freezing/baking, you just didn't care.
Things have been different now for almost 20 years. Since that time junior faculty have been hired by the boatloads and totally changed the tenor of the institution. Not only have they been hired in mass, they have largely succeeded. I would point out as examples HHMI faculty such as Nat Heintz, Jeff Friedman, Bob Darnell (formerly) John Kuriyan, and Stephen Burley. Also people like Titia De Lange and (formerly) Andrej Sali. These people have thrived because they have the benefit of a 72 member faculty with relatively few junior faculty (think of all the Serle awards, sloan fellowships generated by the weight of 6 Nobel laureates, ~25 NAS members, and 12 or so HHMI investigators). They also have the benefit of a 1billion dollar plus endowment for that small faculty size. There is a profusion of interdisciplinary infrastructure (primarily core facilities and lecture series).
Today, RU is one of the most unique biomedical research environments in the world--in my opinion. The concentration of excellent researchers is higher than any other place I have ever worked. There is just no dead wood. And I have worked at at least two other places people would generally also consider for MD/PhD programs. As a result, you will get to know all the famous scientists on campus. You will talk to them at the faculty club, have them on your committee, and play with their dogs on our landscaped campus. The old barriers have long fallen down. During the course of my thesis, I collaborated with 4 different laboratories--some made it to publications, others did not. The key thing is that I was the instigator in each instance and had all the help I wanted. I have never written an email or called a professor, no matter how esteemed, and failed to receive a prompt invitation to discuss the matter in person. The most extreme example of this was when I wrote the President of the University about a model system in his area of scientific expertise and was startled the next day when his secretary called me to arrange a sit down discussion (me only, not my advisor). To me, this is the hallmark of a RU education: even as a graduate student you learn to think and scientfically network by yourself. In some sense you can act as your own PI with your advisor serving as your source of funding. The course requirements and thesis-related bureacracy (i.e. candidacy etc.) is basically minimal. You learn by doing, by reading, and by talking to other people. As a result, you gain scientific judgement and come into your own much earlier.
The downsides to RU? If you are not capable of acting on your own or thinking things through yourself, it is possible for your thesis to get drawn out. Some of the older faculty do not micromanage. However, if you love science and are willing to take risks, this place offers your limitless opportunities. I hate to disagree with Habari, but while there are many collaborations external to the university, there is a ton that occurs internally also. A great example of that is the physics fellows. The fellows, recent Ph.D.s in experimental or theoretical physics, are invited to campus as free standing scholars. They attend seminars and lab meetings and are free to work on any problem they like. They have often catalyzed important interdisciplinary work between labs: e.g. microarray analysis algorithms or enhancer site statistics or single molecular fluoresence studies in vivo. But besides these fellows, you will find limitless opportunity to learn technically from other labs. As Habari noted, there is zero overlap between labs and therefore every reason for people to teach techniques etc (in addition of course to the core research facilities). It is not uncommon for people to do experiments in each others labs--I have done this often and I've helped people from other labs do this too. Sometimes these arrangements become so involved that people set up second benches in other labs.
One other downside: too many great scientists. It is true that the president of the university at RU faces a difficult problem. He controls a lot of money (i.e. endowment funds, philanthropy), and there are a lot of smart profs on campus unaccustomed to hearing "no". Therefore, there can be complicated political concerns occasionally (e.g. new faculty hires), but at the level of a bench scientist, this will never be an issue for you. There is not a professor on campus in whose lab I cannot work.
SO BOTTOM LINE: The "I am consigned to misery" tenor of your OP is totally uncalled for. You should be excited by the possibility of doing your graduate work at such a great place! The people are bright and cooperative; the facilities are fantastic; and the future is also looking good (i.e. new president, new hires).
I am very glad that I did my MD/PhD here. I feel strongly that I wouldn't have had as rich or unique an experience anywhere else. Seriously! It is true that there may exist stronger medical schools than Cornell. However, as an MD-PhD Program, I think the Tri-Institutional Program is terrific and can go toe-to-toe with any other program in the country. The scientific opportunities, both at RU and MSKCC (which is starting a massive building/expansion campaign under Varmus) are fantastic. The clinical curriculum has been great to me too, and the administration ensures we are taken care of (i.e. do not take too long to graduate). The program attracts very scientifically focused, capable students with a tremendous commitment to scientific medicine. The degree has signficantly strengthened my "market value" as I apply to residencies--and I went to what is generally recognized as a top undergrad institution.
Hope that allays your concerns.
